Starting phenix.real_space_refine on Sun Apr 27 06:55:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fr4_50708/04_2025/9fr4_50708.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fr4_50708/04_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_50708/04_2025/9fr4_50708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fr4_50708/04_2025/9fr4_50708.map" model { file = "/net/cci-nas-00/data/ceres_data/9fr4_50708/04_2025/9fr4_50708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fr4_50708/04_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 5.25, per 1000 atoms: 1.08 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: 1.08 Conformation dependent library (CDL) restraints added in 573.0 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: 0.58 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: 1.19 Time building geometry restraints manager: 1.32 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: 5.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.650 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.540 ------------------------------------------------------------------------------- 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 : 0.533 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: 0.2407 time to fit residues: 26.7546 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 : 0.519 ------------------------------------------------------------------------------- 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 = 0.155788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.127045 restraints weight = 5289.450| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.37 r_work: 0.3257 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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 5.354 6812 Z= 0.288 Chirality : 0.045 0.130 696 Planarity : 0.004 0.030 890 Dihedral : 4.247 13.839 690 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 6.59327 ( 336) SS BOND : bond 0.00294 ( 8) SS BOND : angle 0.57066 ( 16) covalent geometry : bond 0.00468 ( 5008) covalent geometry : angle 0.53650 ( 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 : 0.508 Fit side-chains REVERT: B 424 LYS cc_start: 0.8349 (tptt) cc_final: 0.8137 (tptp) REVERT: D 386 LYS cc_start: 0.8009 (mttt) cc_final: 0.7647 (mtpt) REVERT: D 415 THR cc_start: 0.8843 (p) cc_final: 0.8571 (p) REVERT: D 468 ILE cc_start: 0.7566 (pt) cc_final: 0.7333 (tt) REVERT: D 484 GLU cc_start: 0.6896 (tm-30) cc_final: 0.6382 (tm-30) REVERT: C 57 GLU cc_start: 0.7448 (tt0) cc_final: 0.7032 (tt0) outliers start: 12 outliers final: 6 residues processed: 86 average time/residue: 0.2660 time to fit residues: 29.2356 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 : 0.701 ------------------------------------------------------------------------------- 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: 0.2980 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.153033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.126550 restraints weight = 5333.140| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.18 r_work: 0.3265 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5016 Z= 0.165 Angle : 0.499 4.378 6812 Z= 0.268 Chirality : 0.044 0.128 696 Planarity : 0.004 0.028 890 Dihedral : 4.097 13.327 690 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.51 % Allowed : 13.32 % 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: -2.55 (0.31), residues: 606 helix: -5.06 (0.19), residues: 54 sheet: -1.19 (0.32), residues: 210 loop : -1.39 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 353 HIS 0.003 0.001 HIS C 50 PHE 0.021 0.001 PHE D 377 TYR 0.013 0.001 TYR D 495 ARG 0.002 0.000 ARG D 408 Details of bonding type rmsd hydrogen bonds : bond 0.03362 ( 138) hydrogen bonds : angle 6.33883 ( 336) SS BOND : bond 0.00194 ( 8) SS BOND : angle 0.51533 ( 16) covalent geometry : bond 0.00392 ( 5008) covalent geometry : angle 0.49912 ( 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 92 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.478 Fit side-chains REVERT: B 386 LYS cc_start: 0.7865 (mmmt) cc_final: 0.7416 (mtmt) REVERT: B 492 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8374 (mp) REVERT: D 386 LYS cc_start: 0.7984 (mttt) cc_final: 0.7457 (mtpp) REVERT: D 415 THR cc_start: 0.8873 (p) cc_final: 0.8580 (p) REVERT: D 484 GLU cc_start: 0.6839 (tm-30) cc_final: 0.6369 (tm-30) REVERT: C 27 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6530 (pp) REVERT: C 57 GLU cc_start: 0.7508 (tt0) cc_final: 0.7278 (tt0) outliers start: 13 outliers final: 6 residues processed: 87 average time/residue: 0.3080 time to fit residues: 32.8207 Evaluate side-chains 84 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL 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 D residue 371 SER 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: 0.5980 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.157468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.128637 restraints weight = 5350.808| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.37 r_work: 0.3268 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5016 Z= 0.150 Angle : 0.485 4.643 6812 Z= 0.260 Chirality : 0.044 0.128 696 Planarity : 0.003 0.027 890 Dihedral : 3.987 13.260 690 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.32 % Allowed : 15.64 % Favored : 82.05 % 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: -2.27 (0.31), residues: 606 helix: -4.89 (0.27), residues: 52 sheet: -1.09 (0.32), residues: 210 loop : -1.15 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.002 0.000 ARG D 408 Details of bonding type rmsd hydrogen bonds : bond 0.03262 ( 138) hydrogen bonds : angle 6.24038 ( 336) SS BOND : bond 0.00166 ( 8) SS BOND : angle 0.46754 ( 16) covalent geometry : bond 0.00356 ( 5008) covalent geometry : angle 0.48504 ( 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 89 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.487 Fit side-chains REVERT: B 386 LYS cc_start: 0.7839 (mmmt) cc_final: 0.7404 (mtmt) REVERT: A 39 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.6600 (tt0) REVERT: D 386 LYS cc_start: 0.7954 (mttt) cc_final: 0.7403 (mtpp) REVERT: D 415 THR cc_start: 0.8823 (p) cc_final: 0.8574 (p) REVERT: D 484 GLU cc_start: 0.6903 (tm-30) cc_final: 0.6374 (tm-30) REVERT: C 27 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6462 (pp) REVERT: C 57 GLU cc_start: 0.7580 (tt0) cc_final: 0.7341 (tt0) outliers start: 12 outliers final: 5 residues processed: 83 average time/residue: 0.2143 time to fit residues: 21.9020 Evaluate side-chains 80 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 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 27 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 chunk 1 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.153771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.126978 restraints weight = 5361.642| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.21 r_work: 0.3279 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5016 Z= 0.149 Angle : 0.481 4.648 6812 Z= 0.257 Chirality : 0.044 0.128 696 Planarity : 0.003 0.027 890 Dihedral : 3.963 13.309 690 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.28 % Allowed : 15.64 % Favored : 81.08 % 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: -2.03 (0.32), residues: 606 helix: -4.83 (0.29), residues: 52 sheet: -0.90 (0.33), residues: 210 loop : -0.99 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 353 HIS 0.004 0.001 HIS C 50 PHE 0.017 0.001 PHE D 377 TYR 0.011 0.001 TYR D 495 ARG 0.001 0.000 ARG D 408 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 138) hydrogen bonds : angle 6.15535 ( 336) SS BOND : bond 0.00175 ( 8) SS BOND : angle 0.43121 ( 16) covalent geometry : bond 0.00353 ( 5008) covalent geometry : angle 0.48077 ( 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 88 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.499 Fit side-chains REVERT: B 386 LYS cc_start: 0.7838 (mmmt) cc_final: 0.7449 (mtmt) REVERT: B 428 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8040 (p0) REVERT: A 39 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.6576 (tt0) REVERT: D 386 LYS cc_start: 0.8006 (mttt) cc_final: 0.7523 (mtpp) REVERT: D 484 GLU cc_start: 0.6914 (tm-30) cc_final: 0.6385 (tm-30) REVERT: C 27 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6517 (pp) REVERT: C 39 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7046 (tt0) outliers start: 17 outliers final: 8 residues processed: 82 average time/residue: 0.2044 time to fit residues: 21.0016 Evaluate side-chains 82 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 477 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain A residue 12 VAL 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 D residue 406 GLU Chi-restraints excluded: chain C residue 27 LEU 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: 0.8980 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3714 r_free = 0.3714 target = 0.154854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.127989 restraints weight = 5286.521| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.21 r_work: 0.3282 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5016 Z= 0.141 Angle : 0.478 5.109 6812 Z= 0.254 Chirality : 0.043 0.128 696 Planarity : 0.003 0.027 890 Dihedral : 3.899 13.550 690 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.25 % Allowed : 14.67 % Favored : 81.08 % 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: -1.89 (0.32), residues: 606 helix: -4.78 (0.30), residues: 52 sheet: -0.79 (0.33), residues: 210 loop : -0.90 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 353 HIS 0.004 0.001 HIS C 50 PHE 0.017 0.001 PHE D 393 TYR 0.010 0.001 TYR D 495 ARG 0.001 0.000 ARG B 408 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 138) hydrogen bonds : angle 6.11287 ( 336) SS BOND : bond 0.00148 ( 8) SS BOND : angle 0.40999 ( 16) covalent geometry : bond 0.00335 ( 5008) covalent geometry : angle 0.47786 ( 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 96 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.515 Fit side-chains REVERT: B 386 LYS cc_start: 0.7821 (mmmt) cc_final: 0.7437 (mtmt) REVERT: B 428 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8054 (p0) REVERT: A 39 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.6540 (tt0) REVERT: D 386 LYS cc_start: 0.7964 (mttt) cc_final: 0.7495 (mtpp) REVERT: D 484 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6403 (tm-30) REVERT: C 27 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6501 (pp) REVERT: C 39 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7063 (tt0) outliers start: 22 outliers final: 13 residues processed: 88 average time/residue: 0.2044 time to fit residues: 22.3341 Evaluate side-chains 90 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 468 ILE 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 D residue 406 GLU Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 36 optimal weight: 0.0870 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.156184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127437 restraints weight = 5281.841| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.35 r_work: 0.3269 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5016 Z= 0.148 Angle : 0.487 6.684 6812 Z= 0.258 Chirality : 0.044 0.128 696 Planarity : 0.003 0.039 890 Dihedral : 3.934 13.663 690 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.67 % Allowed : 15.83 % Favored : 80.50 % 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: -1.81 (0.32), residues: 606 helix: -4.75 (0.31), residues: 52 sheet: -0.74 (0.33), residues: 210 loop : -0.82 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 353 HIS 0.004 0.001 HIS C 50 PHE 0.016 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 0.03176 ( 138) hydrogen bonds : angle 6.07540 ( 336) SS BOND : bond 0.00151 ( 8) SS BOND : angle 0.42106 ( 16) covalent geometry : bond 0.00355 ( 5008) covalent geometry : angle 0.48672 ( 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: 19 poor density : 73 time to evaluate : 0.532 Fit side-chains REVERT: B 386 LYS cc_start: 0.7784 (mmmt) cc_final: 0.7397 (mtmt) REVERT: B 428 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8032 (p0) REVERT: A 39 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.6524 (tt0) REVERT: D 386 LYS cc_start: 0.7962 (mttt) cc_final: 0.7486 (mtpp) REVERT: D 484 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6415 (tm-30) REVERT: C 27 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6467 (pp) REVERT: C 39 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7050 (tt0) outliers start: 19 outliers final: 15 residues processed: 85 average time/residue: 0.2175 time to fit residues: 22.7276 Evaluate side-chains 90 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 468 ILE 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 27 LEU Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.0870 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.156234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.127557 restraints weight = 5270.868| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.34 r_work: 0.3267 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5016 Z= 0.155 Angle : 0.492 6.525 6812 Z= 0.261 Chirality : 0.044 0.129 696 Planarity : 0.003 0.032 890 Dihedral : 3.950 13.766 690 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.05 % Allowed : 15.25 % 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: -1.77 (0.32), residues: 606 helix: -4.73 (0.31), residues: 52 sheet: -0.70 (0.34), residues: 210 loop : -0.82 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 353 HIS 0.003 0.001 HIS C 50 PHE 0.026 0.001 PHE D 393 TYR 0.010 0.001 TYR D 495 ARG 0.001 0.000 ARG D 457 Details of bonding type rmsd hydrogen bonds : bond 0.03203 ( 138) hydrogen bonds : angle 6.07256 ( 336) SS BOND : bond 0.00161 ( 8) SS BOND : angle 0.42572 ( 16) covalent geometry : bond 0.00370 ( 5008) covalent geometry : angle 0.49233 ( 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 97 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.534 Fit side-chains REVERT: B 386 LYS cc_start: 0.7805 (mmmt) cc_final: 0.7436 (mtmt) REVERT: B 428 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8099 (p0) REVERT: A 39 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.6545 (tt0) REVERT: D 386 LYS cc_start: 0.7954 (mttt) cc_final: 0.7419 (mtpp) REVERT: D 484 GLU cc_start: 0.6910 (tm-30) cc_final: 0.6431 (tm-30) REVERT: C 27 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6490 (pp) REVERT: C 39 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.6970 (tt0) outliers start: 21 outliers final: 15 residues processed: 89 average time/residue: 0.2452 time to fit residues: 26.9589 Evaluate side-chains 94 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 468 ILE 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 27 LEU Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.0050 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.0010 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.5200 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.153761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.127463 restraints weight = 5303.993| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.15 r_work: 0.3297 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2064 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= 0.123 Angle : 0.472 6.383 6812 Z= 0.250 Chirality : 0.043 0.127 696 Planarity : 0.003 0.028 890 Dihedral : 3.825 13.379 690 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.67 % Allowed : 15.44 % 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: -1.70 (0.33), residues: 606 helix: -4.72 (0.30), residues: 52 sheet: -0.63 (0.34), residues: 210 loop : -0.77 (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 0.029 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 0.03057 ( 138) hydrogen bonds : angle 5.95388 ( 336) SS BOND : bond 0.00116 ( 8) SS BOND : angle 0.36354 ( 16) covalent geometry : bond 0.00290 ( 5008) covalent geometry : angle 0.47221 ( 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 95 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.531 Fit side-chains REVERT: B 386 LYS cc_start: 0.7798 (mmmt) cc_final: 0.7463 (mtmt) REVERT: B 428 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8107 (p0) REVERT: A 39 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.6593 (tt0) REVERT: D 386 LYS cc_start: 0.7994 (mttt) cc_final: 0.7524 (mtpp) REVERT: D 484 GLU cc_start: 0.6902 (tm-30) cc_final: 0.6628 (tm-30) REVERT: C 27 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6583 (pp) REVERT: C 39 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7057 (tt0) outliers start: 19 outliers final: 14 residues processed: 89 average time/residue: 0.2110 time to fit residues: 23.1971 Evaluate side-chains 91 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 468 ILE 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 27 LEU Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 86 LEU 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: 0.6980 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 D 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.156892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128154 restraints weight = 5251.965| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.35 r_work: 0.3272 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5016 Z= 0.148 Angle : 0.487 6.289 6812 Z= 0.258 Chirality : 0.044 0.128 696 Planarity : 0.003 0.028 890 Dihedral : 3.891 13.609 690 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.47 % Allowed : 15.64 % 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: -1.68 (0.32), residues: 606 helix: -4.70 (0.31), residues: 52 sheet: -0.59 (0.34), residues: 210 loop : -0.79 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 353 HIS 0.003 0.001 HIS C 50 PHE 0.029 0.001 PHE D 393 TYR 0.010 0.001 TYR D 495 ARG 0.001 0.000 ARG D 408 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 138) hydrogen bonds : angle 6.00090 ( 336) SS BOND : bond 0.00154 ( 8) SS BOND : angle 0.38946 ( 16) covalent geometry : bond 0.00353 ( 5008) covalent geometry : angle 0.48752 ( 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 92 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.538 Fit side-chains REVERT: B 386 LYS cc_start: 0.7759 (mmmt) cc_final: 0.7417 (mtmt) REVERT: B 428 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8082 (p0) REVERT: A 39 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.6521 (tt0) REVERT: D 386 LYS cc_start: 0.7936 (mttt) cc_final: 0.7393 (mtpp) REVERT: D 484 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6705 (tm-30) REVERT: C 27 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6496 (pp) REVERT: C 39 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.6950 (tt0) outliers start: 18 outliers final: 14 residues processed: 85 average time/residue: 0.2386 time to fit residues: 24.9646 Evaluate side-chains 90 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 468 ILE 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 27 LEU Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 34 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 D 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.157452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.128735 restraints weight = 5266.506| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.35 r_work: 0.3278 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5016 Z= 0.131 Angle : 0.476 6.197 6812 Z= 0.253 Chirality : 0.043 0.128 696 Planarity : 0.003 0.028 890 Dihedral : 3.842 13.473 690 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.67 % Allowed : 15.83 % Favored : 80.50 % 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: -1.62 (0.33), residues: 606 helix: -4.68 (0.31), residues: 52 sheet: -0.54 (0.34), residues: 210 loop : -0.75 (0.33), residues: 344 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 0.028 0.001 PHE D 393 TYR 0.009 0.001 TYR D 495 ARG 0.002 0.000 ARG D 357 Details of bonding type rmsd hydrogen bonds : bond 0.03081 ( 138) hydrogen bonds : angle 5.95932 ( 336) SS BOND : bond 0.00126 ( 8) SS BOND : angle 0.36159 ( 16) covalent geometry : bond 0.00312 ( 5008) covalent geometry : angle 0.47673 ( 6796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3849.10 seconds wall clock time: 69 minutes 13.90 seconds (4153.90 seconds total)