Starting phenix.real_space_refine on Sat May 10 03:38:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fr4_50708/05_2025/9fr4_50708.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fr4_50708/05_2025/9fr4_50708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fr4_50708/05_2025/9fr4_50708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fr4_50708/05_2025/9fr4_50708.map" model { file = "/net/cci-nas-00/data/ceres_data/9fr4_50708/05_2025/9fr4_50708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fr4_50708/05_2025/9fr4_50708.cif" } resolution = 3.1 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= 0.049 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 24 5.16 5 C 3114 2.51 5 N 810 2.21 5 O 926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4874 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1504 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 10, 'TRANS': 177} Chain: "A" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 933 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Restraints were copied for chains: D, C Time building chain proxies: 4.71, per 1000 atoms: 0.97 Number of scatterers: 4874 At special positions: 0 Unit cell: (106.38, 69.0921, 101.993, 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 24 16.00 O 926 8.00 N 810 7.00 C 3114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 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: 1.23 Conformation dependent library (CDL) restraints added in 624.4 milliseconds 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1116 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 10 sheets defined 5.5% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.595A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.503A pdb=" N TYR A 112 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 371 removed outlier: 3.596A pdb=" N SER D 371 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'C' and resid 108 through 112 removed outlier: 3.503A pdb=" N TYR C 112 " --> pdb=" O GLU C 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 7.081A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.540A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N HIS A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N MET A 34 " --> pdb=" O HIS A 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 354 through 358 removed outlier: 7.080A pdb=" N ASN D 437 " --> pdb=" O PHE D 374 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N PHE D 374 " --> pdb=" O ASN D 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.540A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N HIS C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N MET C 34 " --> pdb=" O HIS C 50 " (cutoff:3.500A) 138 hydrogen bonds defined for protein. 336 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: 1.25 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1566 1.35 - 1.47: 1412 1.47 - 1.59: 2000 1.59 - 1.71: 0 1.71 - 1.83: 30 Bond restraints: 5008 Sorted by residual: bond pdb=" C LEU D 335 " pdb=" N CYS D 336 " ideal model delta sigma weight residual 1.329 1.364 -0.035 1.60e-02 3.91e+03 4.78e+00 bond pdb=" C LEU B 335 " pdb=" N CYS B 336 " ideal model delta sigma weight residual 1.329 1.364 -0.035 1.60e-02 3.91e+03 4.78e+00 bond pdb=" CA ILE D 410 " pdb=" CB ILE D 410 " ideal model delta sigma weight residual 1.528 1.540 -0.012 1.34e-02 5.57e+03 7.65e-01 bond pdb=" CB THR C 33 " pdb=" CG2 THR C 33 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.30e-01 bond pdb=" CB THR A 33 " pdb=" CG2 THR A 33 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.30e-01 ... (remaining 5003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 6116 1.04 - 2.08: 551 2.08 - 3.12: 93 3.12 - 4.16: 28 4.16 - 5.20: 8 Bond angle restraints: 6796 Sorted by residual: angle pdb=" N ILE D 418 " pdb=" CA ILE D 418 " pdb=" C ILE D 418 " ideal model delta sigma weight residual 112.17 108.54 3.63 9.50e-01 1.11e+00 1.46e+01 angle pdb=" N ILE B 418 " pdb=" CA ILE B 418 " pdb=" C ILE B 418 " ideal model delta sigma weight residual 112.17 108.54 3.63 9.50e-01 1.11e+00 1.46e+01 angle pdb=" N SER A 30 " pdb=" CA SER A 30 " pdb=" C SER A 30 " ideal model delta sigma weight residual 114.12 108.92 5.20 1.39e+00 5.18e-01 1.40e+01 angle pdb=" N SER C 30 " pdb=" CA SER C 30 " pdb=" C SER C 30 " ideal model delta sigma weight residual 114.12 108.92 5.20 1.39e+00 5.18e-01 1.40e+01 angle pdb=" N VAL D 341 " pdb=" CA VAL D 341 " pdb=" C VAL D 341 " ideal model delta sigma weight residual 111.56 108.38 3.18 8.60e-01 1.35e+00 1.37e+01 ... (remaining 6791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.14: 2529 15.14 - 30.29: 299 30.29 - 45.43: 46 45.43 - 60.57: 20 60.57 - 75.72: 8 Dihedral angle restraints: 2902 sinusoidal: 1128 harmonic: 1774 Sorted by residual: dihedral pdb=" CA GLU D 484 " pdb=" CB GLU D 484 " pdb=" CG GLU D 484 " pdb=" CD GLU D 484 " ideal model delta sinusoidal sigma weight residual -60.00 -109.44 49.44 3 1.50e+01 4.44e-03 8.78e+00 dihedral pdb=" CA GLU B 484 " pdb=" CB GLU B 484 " pdb=" CG GLU B 484 " pdb=" CD GLU B 484 " ideal model delta sinusoidal sigma weight residual -60.00 -109.39 49.39 3 1.50e+01 4.44e-03 8.77e+00 dihedral pdb=" CA LYS D 462 " pdb=" CB LYS D 462 " pdb=" CG LYS D 462 " pdb=" CD LYS D 462 " ideal model delta sinusoidal sigma weight residual 180.00 131.15 48.85 3 1.50e+01 4.44e-03 8.70e+00 ... (remaining 2899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 334 0.027 - 0.054: 226 0.054 - 0.081: 78 0.081 - 0.108: 36 0.108 - 0.135: 22 Chirality restraints: 696 Sorted by residual: chirality pdb=" CA ILE D 434 " pdb=" N ILE D 434 " pdb=" C ILE D 434 " pdb=" CB ILE D 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE D 410 " pdb=" N ILE D 410 " pdb=" C ILE D 410 " pdb=" CB ILE D 410 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 693 not shown) Planarity restraints: 890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 40 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.84e+00 pdb=" N PRO C 41 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 40 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO A 41 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 377 " -0.004 2.00e-02 2.50e+03 8.82e-03 1.36e+00 pdb=" CG PHE D 377 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE D 377 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE D 377 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE D 377 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 377 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE D 377 " 0.000 2.00e-02 2.50e+03 ... (remaining 887 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 105 2.68 - 3.24: 4291 3.24 - 3.79: 7143 3.79 - 4.35: 10268 4.35 - 4.90: 17802 Nonbonded interactions: 39609 Sorted by model distance: nonbonded pdb=" OE2 GLU D 406 " pdb=" OH TYR D 495 " model vdw 2.125 3.040 nonbonded pdb=" OE2 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.126 3.040 nonbonded pdb=" OG1 THR C 91 " pdb=" O VAL C 121 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR A 91 " pdb=" O VAL A 121 " model vdw 2.235 3.040 nonbonded pdb=" NH2 ARG D 454 " pdb=" O SER D 469 " model vdw 2.253 3.120 ... (remaining 39604 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: 0.03 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } 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: 9.370 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: 0.460 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 17.010 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 0.035 5016 Z= 0.196 Angle : 0.678 5.204 6812 Z= 0.433 Chirality : 0.045 0.135 696 Planarity : 0.003 0.034 890 Dihedral : 13.900 75.716 1762 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % 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: -3.57 (0.28), residues: 606 helix: -5.28 (0.13), residues: 52 sheet: -1.59 (0.32), residues: 212 loop : -2.45 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 436 HIS 0.003 0.001 HIS A 50 PHE 0.019 0.001 PHE D 377 TYR 0.009 0.001 TYR B 495 ARG 0.002 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.12674 ( 138) hydrogen bonds : angle 8.08718 ( 336) SS BOND : bond 0.00190 ( 8) SS BOND : angle 0.55442 ( 16) covalent geometry : bond 0.00409 ( 5008) covalent geometry : angle 0.67825 ( 6796) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.547 Fit side-chains REVERT: B 424 LYS cc_start: 0.8444 (tptt) cc_final: 0.8234 (tptp) REVERT: D 386 LYS cc_start: 0.8261 (mttt) cc_final: 0.7983 (mtpt) REVERT: D 415 THR cc_start: 0.8757 (p) cc_final: 0.8439 (p) REVERT: C 17 SER cc_start: 0.7210 (m) cc_final: 0.6856 (p) REVERT: C 57 GLU cc_start: 0.7359 (tt0) cc_final: 0.6695 (pt0) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2219 time to fit residues: 24.6208 Evaluate side-chains 81 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN B 487 ASN D 360 ASN D 487 ASN C 3 GLN C 74 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.155694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.126999 restraints weight = 5289.435| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.36 r_work: 0.3256 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5016 Z= 0.196 Angle : 0.537 5.356 6812 Z= 0.288 Chirality : 0.045 0.130 696 Planarity : 0.004 0.030 890 Dihedral : 4.247 13.838 690 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.32 % Allowed : 11.00 % Favored : 86.68 % 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: -2.97 (0.29), residues: 606 helix: -5.20 (0.14), residues: 54 sheet: -1.34 (0.31), residues: 212 loop : -1.81 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 353 HIS 0.003 0.001 HIS A 50 PHE 0.023 0.002 PHE D 377 TYR 0.014 0.002 TYR D 495 ARG 0.003 0.000 ARG D 408 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 138) hydrogen bonds : angle 6.59293 ( 336) SS BOND : bond 0.00294 ( 8) SS BOND : angle 0.57035 ( 16) covalent geometry : bond 0.00468 ( 5008) covalent geometry : angle 0.53654 ( 6796) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.575 Fit side-chains REVERT: B 424 LYS cc_start: 0.8345 (tptt) cc_final: 0.8132 (tptp) REVERT: D 386 LYS cc_start: 0.8004 (mttt) cc_final: 0.7640 (mtpt) REVERT: D 415 THR cc_start: 0.8840 (p) cc_final: 0.8568 (p) REVERT: D 468 ILE cc_start: 0.7564 (pt) cc_final: 0.7330 (tt) REVERT: D 484 GLU cc_start: 0.6895 (tm-30) cc_final: 0.6382 (tm-30) REVERT: C 57 GLU cc_start: 0.7444 (tt0) cc_final: 0.7030 (tt0) outliers start: 12 outliers final: 6 residues processed: 86 average time/residue: 0.2098 time to fit residues: 22.2376 Evaluate side-chains 82 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain C residue 12 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 53 optimal weight: 0.0870 chunk 21 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 ASN A 117 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.155465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128864 restraints weight = 5295.251| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.19 r_work: 0.3291 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5016 Z= 0.133 Angle : 0.471 3.883 6812 Z= 0.253 Chirality : 0.043 0.128 696 Planarity : 0.003 0.028 890 Dihedral : 3.909 12.792 690 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.12 % Allowed : 13.71 % Favored : 84.17 % 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: -2.49 (0.31), residues: 606 helix: -5.08 (0.18), residues: 54 sheet: -1.14 (0.32), residues: 210 loop : -1.36 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 353 HIS 0.003 0.001 HIS C 50 PHE 0.017 0.001 PHE D 377 TYR 0.012 0.001 TYR D 495 ARG 0.001 0.000 ARG C 108 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 138) hydrogen bonds : angle 6.19602 ( 336) SS BOND : bond 0.00141 ( 8) SS BOND : angle 0.44380 ( 16) covalent geometry : bond 0.00314 ( 5008) covalent geometry : angle 0.47133 ( 6796) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.550 Fit side-chains REVERT: B 386 LYS cc_start: 0.7815 (mmmt) cc_final: 0.7371 (mtmt) REVERT: D 386 LYS cc_start: 0.7893 (mttt) cc_final: 0.7479 (mtpt) REVERT: D 415 THR cc_start: 0.8856 (p) cc_final: 0.8569 (p) REVERT: D 468 ILE cc_start: 0.7594 (pt) cc_final: 0.7361 (tt) REVERT: D 484 GLU cc_start: 0.6823 (tm-30) cc_final: 0.6394 (tm-30) REVERT: C 27 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6505 (pp) REVERT: C 57 GLU cc_start: 0.7542 (tt0) cc_final: 0.7307 (tt0) outliers start: 11 outliers final: 5 residues processed: 85 average time/residue: 0.2394 time to fit residues: 24.9191 Evaluate side-chains 81 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 27 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 51 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 45 optimal weight: 0.0070 chunk 12 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 26 optimal weight: 0.0470 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.158057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.131505 restraints weight = 5310.883| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.18 r_work: 0.3323 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 5016 Z= 0.095 Angle : 0.435 3.730 6812 Z= 0.234 Chirality : 0.042 0.128 696 Planarity : 0.003 0.027 890 Dihedral : 3.608 12.355 690 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.93 % Allowed : 15.06 % Favored : 83.01 % 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: -2.11 (0.32), residues: 606 helix: -5.01 (0.18), residues: 54 sheet: -0.85 (0.33), residues: 210 loop : -1.06 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 353 HIS 0.004 0.001 HIS C 50 PHE 0.014 0.001 PHE D 393 TYR 0.008 0.001 TYR D 495 ARG 0.001 0.000 ARG D 408 Details of bonding type rmsd hydrogen bonds : bond 0.02992 ( 138) hydrogen bonds : angle 5.93664 ( 336) SS BOND : bond 0.00098 ( 8) SS BOND : angle 0.30133 ( 16) covalent geometry : bond 0.00218 ( 5008) covalent geometry : angle 0.43508 ( 6796) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.563 Fit side-chains REVERT: B 386 LYS cc_start: 0.7768 (mmmt) cc_final: 0.7405 (mtmt) REVERT: A 39 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.6463 (tt0) REVERT: D 386 LYS cc_start: 0.7908 (mttt) cc_final: 0.7538 (mtpt) REVERT: D 415 THR cc_start: 0.8847 (p) cc_final: 0.8601 (p) REVERT: D 468 ILE cc_start: 0.7522 (pt) cc_final: 0.7258 (tt) REVERT: D 484 GLU cc_start: 0.6879 (tm-30) cc_final: 0.6438 (tm-30) REVERT: C 57 GLU cc_start: 0.7596 (tt0) cc_final: 0.7354 (tt0) REVERT: C 106 TYR cc_start: 0.8658 (p90) cc_final: 0.8416 (p90) REVERT: C 108 ARG cc_start: 0.7590 (mtm-85) cc_final: 0.7191 (mtt180) outliers start: 10 outliers final: 4 residues processed: 89 average time/residue: 0.2070 time to fit residues: 22.7946 Evaluate side-chains 84 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain D residue 398 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 26 optimal weight: 0.0980 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.155394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.128617 restraints weight = 5378.436| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.20 r_work: 0.3302 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5016 Z= 0.130 Angle : 0.461 4.873 6812 Z= 0.246 Chirality : 0.043 0.127 696 Planarity : 0.003 0.027 890 Dihedral : 3.720 12.994 690 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.90 % Allowed : 15.44 % Favored : 81.66 % 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: -1.90 (0.32), residues: 606 helix: -4.91 (0.21), residues: 52 sheet: -0.77 (0.32), residues: 210 loop : -0.90 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 353 HIS 0.003 0.001 HIS C 50 PHE 0.017 0.001 PHE D 393 TYR 0.009 0.001 TYR D 495 ARG 0.001 0.000 ARG D 408 Details of bonding type rmsd hydrogen bonds : bond 0.03099 ( 138) hydrogen bonds : angle 5.99965 ( 336) SS BOND : bond 0.00148 ( 8) SS BOND : angle 0.40342 ( 16) covalent geometry : bond 0.00308 ( 5008) covalent geometry : angle 0.46123 ( 6796) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.524 Fit side-chains REVERT: B 386 LYS cc_start: 0.7807 (mmmt) cc_final: 0.7452 (mtmt) REVERT: B 428 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7917 (p0) REVERT: A 39 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.6534 (tt0) REVERT: D 386 LYS cc_start: 0.7964 (mttt) cc_final: 0.7599 (mtpp) REVERT: D 415 THR cc_start: 0.8834 (p) cc_final: 0.8602 (p) REVERT: D 468 ILE cc_start: 0.7586 (pt) cc_final: 0.7369 (tt) REVERT: D 484 GLU cc_start: 0.6874 (tm-30) cc_final: 0.6389 (tm-30) REVERT: C 39 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7010 (tt0) REVERT: C 57 GLU cc_start: 0.7600 (tt0) cc_final: 0.7365 (tt0) REVERT: C 106 TYR cc_start: 0.8785 (p90) cc_final: 0.8568 (p90) outliers start: 15 outliers final: 8 residues processed: 85 average time/residue: 0.2026 time to fit residues: 21.6399 Evaluate side-chains 83 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain C residue 39 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 ASN D 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.155211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.128447 restraints weight = 5292.048| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.20 r_work: 0.3287 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5016 Z= 0.152 Angle : 0.481 4.919 6812 Z= 0.256 Chirality : 0.044 0.128 696 Planarity : 0.003 0.028 890 Dihedral : 3.898 12.975 690 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.09 % Allowed : 15.44 % Favored : 81.47 % 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: -1.83 (0.32), residues: 606 helix: -4.83 (0.25), residues: 54 sheet: -0.68 (0.33), residues: 210 loop : -0.86 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 353 HIS 0.003 0.001 HIS C 50 PHE 0.017 0.001 PHE D 377 TYR 0.010 0.001 TYR D 495 ARG 0.001 0.000 ARG D 408 Details of bonding type rmsd hydrogen bonds : bond 0.03208 ( 138) hydrogen bonds : angle 6.04703 ( 336) SS BOND : bond 0.00179 ( 8) SS BOND : angle 0.44156 ( 16) covalent geometry : bond 0.00361 ( 5008) covalent geometry : angle 0.48087 ( 6796) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.533 Fit side-chains REVERT: B 386 LYS cc_start: 0.7831 (mmmt) cc_final: 0.7443 (mtmt) REVERT: B 428 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8048 (p0) REVERT: A 39 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.6534 (tt0) REVERT: D 386 LYS cc_start: 0.7954 (mttt) cc_final: 0.7595 (mtpp) REVERT: D 484 GLU cc_start: 0.6892 (tm-30) cc_final: 0.6382 (tm-30) REVERT: C 39 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7001 (tt0) REVERT: C 106 TYR cc_start: 0.8789 (p90) cc_final: 0.8575 (p90) outliers start: 16 outliers final: 8 residues processed: 85 average time/residue: 0.2206 time to fit residues: 23.2242 Evaluate side-chains 84 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain C residue 39 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 1 optimal weight: 0.0970 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 0.0470 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.160844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.132020 restraints weight = 5211.645| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.35 r_work: 0.3312 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5016 Z= 0.094 Angle : 0.447 6.608 6812 Z= 0.236 Chirality : 0.042 0.127 696 Planarity : 0.003 0.027 890 Dihedral : 3.618 12.248 690 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.70 % Allowed : 15.83 % Favored : 81.47 % 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: -1.61 (0.33), residues: 606 helix: -4.78 (0.25), residues: 52 sheet: -0.52 (0.33), residues: 210 loop : -0.73 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS C 50 PHE 0.012 0.001 PHE D 393 TYR 0.006 0.001 TYR D 489 ARG 0.001 0.000 ARG D 357 Details of bonding type rmsd hydrogen bonds : bond 0.02912 ( 138) hydrogen bonds : angle 5.87394 ( 336) SS BOND : bond 0.00085 ( 8) SS BOND : angle 0.31061 ( 16) covalent geometry : bond 0.00217 ( 5008) covalent geometry : angle 0.44715 ( 6796) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.597 Fit side-chains REVERT: B 386 LYS cc_start: 0.7757 (mmmt) cc_final: 0.7379 (mtmt) REVERT: B 428 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8033 (p0) REVERT: A 39 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.6455 (tt0) REVERT: D 386 LYS cc_start: 0.7844 (mttt) cc_final: 0.7537 (mtpt) REVERT: D 484 GLU cc_start: 0.6928 (tm-30) cc_final: 0.6683 (tm-30) REVERT: C 39 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.6976 (tt0) REVERT: C 106 TYR cc_start: 0.8742 (p90) cc_final: 0.8534 (p90) outliers start: 14 outliers final: 7 residues processed: 88 average time/residue: 0.2286 time to fit residues: 24.4680 Evaluate side-chains 85 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain C residue 39 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 26 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.0070 chunk 19 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 ASN D 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.156852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.130107 restraints weight = 5300.391| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.20 r_work: 0.3300 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5016 Z= 0.128 Angle : 0.468 6.387 6812 Z= 0.248 Chirality : 0.043 0.128 696 Planarity : 0.003 0.028 890 Dihedral : 3.727 12.441 690 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.90 % Allowed : 16.41 % Favored : 80.69 % 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: -1.63 (0.32), residues: 606 helix: -4.73 (0.28), residues: 54 sheet: -0.49 (0.33), residues: 210 loop : -0.76 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 353 HIS 0.003 0.001 HIS C 50 PHE 0.029 0.001 PHE D 393 TYR 0.008 0.001 TYR D 495 ARG 0.001 0.000 ARG D 408 Details of bonding type rmsd hydrogen bonds : bond 0.03033 ( 138) hydrogen bonds : angle 5.88002 ( 336) SS BOND : bond 0.00131 ( 8) SS BOND : angle 0.38711 ( 16) covalent geometry : bond 0.00303 ( 5008) covalent geometry : angle 0.46846 ( 6796) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.511 Fit side-chains REVERT: B 386 LYS cc_start: 0.7826 (mmmt) cc_final: 0.7464 (mtmt) REVERT: B 428 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8151 (p0) REVERT: A 39 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.6484 (tt0) REVERT: D 386 LYS cc_start: 0.7958 (mttt) cc_final: 0.7645 (mtpt) REVERT: D 484 GLU cc_start: 0.6961 (tm-30) cc_final: 0.6733 (tm-30) REVERT: C 39 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.6978 (tt0) REVERT: C 65 LYS cc_start: 0.6707 (mmtt) cc_final: 0.6351 (mmtt) outliers start: 15 outliers final: 9 residues processed: 89 average time/residue: 0.2221 time to fit residues: 24.0155 Evaluate side-chains 88 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain C residue 39 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 0.0030 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 49 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 ASN D 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.159782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.131120 restraints weight = 5225.644| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.34 r_work: 0.3302 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5016 Z= 0.114 Angle : 0.456 6.284 6812 Z= 0.242 Chirality : 0.043 0.127 696 Planarity : 0.003 0.028 890 Dihedral : 3.653 12.589 690 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.12 % Allowed : 16.22 % Favored : 81.66 % 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: -1.57 (0.33), residues: 606 helix: -4.71 (0.28), residues: 54 sheet: -0.43 (0.34), residues: 210 loop : -0.73 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 353 HIS 0.003 0.001 HIS C 50 PHE 0.026 0.001 PHE D 393 TYR 0.007 0.001 TYR D 495 ARG 0.002 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 138) hydrogen bonds : angle 5.76544 ( 336) SS BOND : bond 0.00111 ( 8) SS BOND : angle 0.33620 ( 16) covalent geometry : bond 0.00269 ( 5008) covalent geometry : angle 0.45657 ( 6796) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.559 Fit side-chains REVERT: B 386 LYS cc_start: 0.7819 (mmmt) cc_final: 0.7432 (mtmt) REVERT: B 428 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8067 (p0) REVERT: A 39 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.6500 (tt0) REVERT: A 108 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7307 (mtt180) REVERT: D 386 LYS cc_start: 0.7875 (mttt) cc_final: 0.7562 (mtpt) REVERT: D 484 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6720 (tm-30) REVERT: C 39 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.6909 (tt0) REVERT: C 65 LYS cc_start: 0.6667 (mmtt) cc_final: 0.6302 (mmtt) REVERT: C 108 ARG cc_start: 0.7612 (mtm-85) cc_final: 0.7236 (mtt180) outliers start: 11 outliers final: 7 residues processed: 84 average time/residue: 0.2303 time to fit residues: 23.4988 Evaluate side-chains 85 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain C residue 39 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 12 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 ASN D 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.157700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131013 restraints weight = 5238.516| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.18 r_work: 0.3314 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5016 Z= 0.112 Angle : 0.457 6.158 6812 Z= 0.243 Chirality : 0.043 0.127 696 Planarity : 0.003 0.028 890 Dihedral : 3.603 12.141 690 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.32 % Allowed : 16.41 % Favored : 81.27 % 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: -1.49 (0.33), residues: 606 helix: -4.67 (0.30), residues: 54 sheet: -0.34 (0.34), residues: 210 loop : -0.70 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 353 HIS 0.003 0.001 HIS C 50 PHE 0.026 0.001 PHE D 393 TYR 0.006 0.001 TYR D 495 ARG 0.002 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.02986 ( 138) hydrogen bonds : angle 5.82270 ( 336) SS BOND : bond 0.00099 ( 8) SS BOND : angle 0.33049 ( 16) covalent geometry : bond 0.00262 ( 5008) covalent geometry : angle 0.45775 ( 6796) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.538 Fit side-chains REVERT: B 386 LYS cc_start: 0.7829 (mmmt) cc_final: 0.7475 (mtmt) REVERT: B 428 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8094 (p0) REVERT: A 39 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.6502 (tt0) REVERT: D 386 LYS cc_start: 0.7919 (mttt) cc_final: 0.7617 (mtpt) REVERT: D 484 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6791 (tm-30) REVERT: C 39 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.6941 (tt0) REVERT: C 65 LYS cc_start: 0.6705 (mmtt) cc_final: 0.6332 (mmtt) outliers start: 12 outliers final: 8 residues processed: 85 average time/residue: 0.2545 time to fit residues: 26.3269 Evaluate side-chains 86 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain C residue 39 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 0.0370 chunk 57 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN D 360 ASN D 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.159592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.130793 restraints weight = 5245.782| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.33 r_work: 0.3297 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5016 Z= 0.119 Angle : 0.465 6.147 6812 Z= 0.246 Chirality : 0.043 0.128 696 Planarity : 0.003 0.028 890 Dihedral : 3.653 12.308 690 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.51 % Allowed : 16.60 % Favored : 80.89 % 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: -1.45 (0.33), residues: 606 helix: -4.64 (0.31), residues: 54 sheet: -0.30 (0.34), residues: 210 loop : -0.68 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 353 HIS 0.003 0.001 HIS C 50 PHE 0.025 0.001 PHE D 393 TYR 0.007 0.001 TYR D 495 ARG 0.002 0.000 ARG D 357 Details of bonding type rmsd hydrogen bonds : bond 0.03031 ( 138) hydrogen bonds : angle 5.84877 ( 336) SS BOND : bond 0.00117 ( 8) SS BOND : angle 0.34522 ( 16) covalent geometry : bond 0.00280 ( 5008) covalent geometry : angle 0.46520 ( 6796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3200.40 seconds wall clock time: 56 minutes 35.53 seconds (3395.53 seconds total)