Starting phenix.real_space_refine on Wed Sep 17 05:13:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fr4_50708/09_2025/9fr4_50708.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fr4_50708/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9fr4_50708/09_2025/9fr4_50708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fr4_50708/09_2025/9fr4_50708.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fr4_50708/09_2025/9fr4_50708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fr4_50708/09_2025/9fr4_50708.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.049 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.50, per 1000 atoms: 0.31 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: 0.26 Conformation dependent library (CDL) restraints added in 187.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.17 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: 0.69 Time building geometry restraints manager: 0.42 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: 0.01 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: 5.900 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.540 Find NCS groups from input model: 0.040 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.880 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.002 0.000 ARG C 72 TYR 0.009 0.001 TYR B 495 PHE 0.019 0.001 PHE D 377 TRP 0.011 0.002 TRP D 436 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 5008) covalent geometry : angle 0.67825 ( 6796) SS BOND : bond 0.00190 ( 8) SS BOND : angle 0.55442 ( 16) hydrogen bonds : bond 0.12674 ( 138) hydrogen bonds : angle 8.08718 ( 336) *********************** 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 : 0.219 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: 0.1093 time to fit residues: 12.1373 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 : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 0.0370 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.154640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.126568 restraints weight = 5338.498| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.32 r_work: 0.3274 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1137 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= 0.167 Angle : 0.511 4.840 6812 Z= 0.275 Chirality : 0.044 0.130 696 Planarity : 0.004 0.030 890 Dihedral : 4.102 13.469 690 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.12 % Allowed : 10.42 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.93 (0.29), residues: 606 helix: -5.21 (0.14), residues: 54 sheet: -1.36 (0.31), residues: 210 loop : -1.75 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 403 TYR 0.013 0.001 TYR D 495 PHE 0.020 0.001 PHE D 377 TRP 0.010 0.002 TRP B 353 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 5008) covalent geometry : angle 0.51132 ( 6796) SS BOND : bond 0.00253 ( 8) SS BOND : angle 0.55814 ( 16) hydrogen bonds : bond 0.03451 ( 138) hydrogen bonds : angle 6.51090 ( 336) *********************** 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 93 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.186 Fit side-chains REVERT: B 386 LYS cc_start: 0.7787 (mmmt) cc_final: 0.7314 (mtmt) REVERT: B 489 TYR cc_start: 0.8671 (m-80) cc_final: 0.8422 (m-80) REVERT: D 386 LYS cc_start: 0.7968 (mttt) cc_final: 0.7599 (mtpt) REVERT: D 403 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8266 (mtp180) REVERT: D 415 THR cc_start: 0.8832 (p) cc_final: 0.8564 (p) REVERT: D 468 ILE cc_start: 0.7528 (pt) cc_final: 0.7271 (tt) REVERT: D 484 GLU cc_start: 0.6789 (tm-30) cc_final: 0.6299 (tm-30) REVERT: C 57 GLU cc_start: 0.7436 (tt0) cc_final: 0.6498 (pt0) outliers start: 11 outliers final: 4 residues processed: 87 average time/residue: 0.0966 time to fit residues: 10.3753 Evaluate side-chains 80 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 398 ASP Chi-restraints excluded: chain D residue 403 ARG 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 44 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 0.0570 chunk 36 optimal weight: 0.5980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN A 117 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.154705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.127935 restraints weight = 5345.386| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.23 r_work: 0.3284 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1460 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= 0.153 Angle : 0.485 4.015 6812 Z= 0.261 Chirality : 0.044 0.127 696 Planarity : 0.004 0.028 890 Dihedral : 4.004 13.038 690 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.51 % Allowed : 13.71 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.31), residues: 606 helix: -5.13 (0.16), residues: 54 sheet: -1.15 (0.32), residues: 210 loop : -1.38 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 408 TYR 0.011 0.001 TYR D 495 PHE 0.020 0.001 PHE D 377 TRP 0.012 0.002 TRP D 353 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 5008) covalent geometry : angle 0.48547 ( 6796) SS BOND : bond 0.00176 ( 8) SS BOND : angle 0.48747 ( 16) hydrogen bonds : bond 0.03296 ( 138) hydrogen bonds : angle 6.27645 ( 336) *********************** 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 91 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.194 Fit side-chains REVERT: B 386 LYS cc_start: 0.7853 (mmmt) cc_final: 0.7401 (mtmt) REVERT: B 489 TYR cc_start: 0.8734 (m-80) cc_final: 0.8463 (m-80) REVERT: D 386 LYS cc_start: 0.7919 (mttt) cc_final: 0.7535 (mtpt) REVERT: D 415 THR cc_start: 0.8863 (p) cc_final: 0.8582 (p) REVERT: D 468 ILE cc_start: 0.7623 (pt) cc_final: 0.7406 (tt) REVERT: D 484 GLU cc_start: 0.6811 (tm-30) cc_final: 0.6382 (tm-30) REVERT: C 27 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6494 (pp) REVERT: C 57 GLU cc_start: 0.7516 (tt0) cc_final: 0.7287 (tt0) outliers start: 13 outliers final: 8 residues processed: 84 average time/residue: 0.1062 time to fit residues: 10.8399 Evaluate side-chains 85 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 345 THR Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 403 ARG 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 22 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 ASN B 474 GLN D 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.153481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.126825 restraints weight = 5345.999| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.21 r_work: 0.3268 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5016 Z= 0.178 Angle : 0.504 5.012 6812 Z= 0.271 Chirality : 0.044 0.128 696 Planarity : 0.004 0.033 890 Dihedral : 4.123 13.325 690 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.47 % Allowed : 14.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.31), residues: 606 helix: -5.05 (0.18), residues: 54 sheet: -1.07 (0.32), residues: 210 loop : -1.23 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 408 TYR 0.013 0.001 TYR D 495 PHE 0.021 0.001 PHE D 377 TRP 0.012 0.002 TRP D 353 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 5008) covalent geometry : angle 0.50375 ( 6796) SS BOND : bond 0.00213 ( 8) SS BOND : angle 0.54267 ( 16) hydrogen bonds : bond 0.03348 ( 138) hydrogen bonds : angle 6.32638 ( 336) *********************** 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 98 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.177 Fit side-chains REVERT: B 386 LYS cc_start: 0.7874 (mmmt) cc_final: 0.7429 (mtmt) REVERT: B 489 TYR cc_start: 0.8687 (m-80) cc_final: 0.8441 (m-80) REVERT: A 39 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.6589 (tt0) REVERT: D 386 LYS cc_start: 0.7999 (mttt) cc_final: 0.7452 (mtpp) REVERT: D 415 THR cc_start: 0.8833 (p) cc_final: 0.8587 (p) REVERT: D 468 ILE cc_start: 0.7682 (pt) cc_final: 0.7482 (tt) REVERT: D 484 GLU cc_start: 0.6878 (tm-30) cc_final: 0.6364 (tm-30) REVERT: C 27 LEU cc_start: 0.6760 (OUTLIER) cc_final: 0.6476 (pp) REVERT: C 57 GLU cc_start: 0.7542 (tt0) cc_final: 0.7305 (tt0) outliers start: 18 outliers final: 9 residues processed: 88 average time/residue: 0.0978 time to fit residues: 10.5224 Evaluate side-chains 87 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL 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 345 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 403 ARG 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 47 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.155635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.126766 restraints weight = 5329.747| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.35 r_work: 0.3248 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5016 Z= 0.203 Angle : 0.528 5.555 6812 Z= 0.282 Chirality : 0.045 0.129 696 Planarity : 0.004 0.036 890 Dihedral : 4.264 14.279 690 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.47 % Allowed : 14.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.32), residues: 606 helix: -4.93 (0.25), residues: 52 sheet: -0.99 (0.33), residues: 210 loop : -1.10 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 457 TYR 0.013 0.001 TYR D 495 PHE 0.022 0.001 PHE D 377 TRP 0.013 0.002 TRP D 353 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 5008) covalent geometry : angle 0.52844 ( 6796) SS BOND : bond 0.00239 ( 8) SS BOND : angle 0.54419 ( 16) hydrogen bonds : bond 0.03464 ( 138) hydrogen bonds : angle 6.37220 ( 336) *********************** 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 97 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.187 Fit side-chains REVERT: B 386 LYS cc_start: 0.7846 (mmmt) cc_final: 0.7387 (mtmt) REVERT: B 428 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8043 (p0) REVERT: B 489 TYR cc_start: 0.8725 (m-80) cc_final: 0.8477 (m-80) REVERT: A 39 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.6607 (tt0) REVERT: D 386 LYS cc_start: 0.7995 (mttt) cc_final: 0.7445 (mtpp) REVERT: D 484 GLU cc_start: 0.6944 (tm-30) cc_final: 0.6403 (tm-30) REVERT: C 27 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6507 (pp) REVERT: C 39 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7031 (tt0) outliers start: 18 outliers final: 10 residues processed: 88 average time/residue: 0.1091 time to fit residues: 11.6760 Evaluate side-chains 90 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 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 371 SER 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 51 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 46 optimal weight: 0.0470 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 ASN D 481 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 = 0.154949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.128043 restraints weight = 5325.271| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.21 r_work: 0.3284 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1866 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= 0.131 Angle : 0.475 4.748 6812 Z= 0.254 Chirality : 0.043 0.128 696 Planarity : 0.003 0.039 890 Dihedral : 3.951 13.168 690 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.44 % Allowed : 14.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.32), residues: 606 helix: -4.86 (0.25), residues: 52 sheet: -0.83 (0.33), residues: 210 loop : -0.92 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 408 TYR 0.009 0.001 TYR D 495 PHE 0.017 0.001 PHE D 393 TRP 0.010 0.002 TRP B 436 HIS 0.004 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 5008) covalent geometry : angle 0.47467 ( 6796) SS BOND : bond 0.00127 ( 8) SS BOND : angle 0.40393 ( 16) hydrogen bonds : bond 0.03169 ( 138) hydrogen bonds : angle 6.13899 ( 336) *********************** 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 103 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.150 Fit side-chains REVERT: B 386 LYS cc_start: 0.7805 (mmmt) cc_final: 0.7402 (mtmt) REVERT: B 428 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8039 (p0) REVERT: A 39 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.6532 (tt0) REVERT: D 386 LYS cc_start: 0.7960 (mttt) cc_final: 0.7440 (mtpp) REVERT: D 484 GLU cc_start: 0.6925 (tm-30) cc_final: 0.6408 (tm-30) REVERT: C 27 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6528 (pp) REVERT: C 39 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7029 (tt0) outliers start: 23 outliers final: 12 residues processed: 95 average time/residue: 0.0998 time to fit residues: 11.5437 Evaluate side-chains 95 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 THR 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 403 ARG 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 5 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 0.0870 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.0170 chunk 13 optimal weight: 0.0970 overall best weight: 0.3194 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.158335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.131557 restraints weight = 5334.365| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.22 r_work: 0.3320 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2072 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= 0.092 Angle : 0.435 3.965 6812 Z= 0.234 Chirality : 0.042 0.130 696 Planarity : 0.003 0.027 890 Dihedral : 3.600 12.264 690 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.09 % Allowed : 16.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.33), residues: 606 helix: -4.84 (0.23), residues: 54 sheet: -0.66 (0.34), residues: 210 loop : -0.76 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 403 TYR 0.009 0.001 TYR B 489 PHE 0.016 0.001 PHE D 393 TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 5008) covalent geometry : angle 0.43510 ( 6796) SS BOND : bond 0.00078 ( 8) SS BOND : angle 0.30988 ( 16) hydrogen bonds : bond 0.02875 ( 138) hydrogen bonds : angle 5.79916 ( 336) *********************** 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 98 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.187 Fit side-chains REVERT: B 386 LYS cc_start: 0.7801 (mmmt) cc_final: 0.7432 (mtmt) REVERT: B 428 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8084 (p0) REVERT: A 39 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.6414 (tt0) REVERT: D 386 LYS cc_start: 0.7926 (mttt) cc_final: 0.7584 (mtpp) REVERT: D 403 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8318 (mtp180) REVERT: D 457 ARG cc_start: 0.8794 (ttt90) cc_final: 0.8578 (ttt180) REVERT: D 484 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6811 (tm-30) REVERT: C 27 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6589 (pp) REVERT: C 39 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.6972 (tt0) REVERT: C 108 ARG cc_start: 0.7611 (mtm-85) cc_final: 0.7248 (mtt180) outliers start: 16 outliers final: 5 residues processed: 93 average time/residue: 0.1165 time to fit residues: 12.9382 Evaluate side-chains 91 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 468 ILE 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 398 ASP Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain C residue 27 LEU 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 43 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 ASN D 481 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 = 0.153436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.126643 restraints weight = 5380.427| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.22 r_work: 0.3254 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5016 Z= 0.215 Angle : 0.542 6.618 6812 Z= 0.288 Chirality : 0.046 0.132 696 Planarity : 0.004 0.030 890 Dihedral : 4.193 14.348 690 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.28 % Allowed : 15.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.32), residues: 606 helix: -4.79 (0.29), residues: 54 sheet: -0.74 (0.33), residues: 210 loop : -0.91 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 403 TYR 0.010 0.002 TYR D 495 PHE 0.023 0.002 PHE D 377 TRP 0.013 0.002 TRP D 353 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 5008) covalent geometry : angle 0.54239 ( 6796) SS BOND : bond 0.00244 ( 8) SS BOND : angle 0.54457 ( 16) hydrogen bonds : bond 0.03493 ( 138) hydrogen bonds : angle 6.21878 ( 336) *********************** 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: 17 poor density : 76 time to evaluate : 0.202 Fit side-chains REVERT: B 386 LYS cc_start: 0.7862 (mmmt) cc_final: 0.7488 (mtmt) REVERT: B 428 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8069 (p0) REVERT: A 39 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.6593 (tt0) REVERT: D 386 LYS cc_start: 0.7983 (mttt) cc_final: 0.7497 (mtpp) REVERT: D 484 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6553 (tm-30) REVERT: C 27 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6534 (pp) REVERT: C 39 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7015 (tt0) outliers start: 17 outliers final: 10 residues processed: 86 average time/residue: 0.1004 time to fit residues: 10.4221 Evaluate side-chains 87 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 16 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 0.0170 chunk 18 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.158443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.129717 restraints weight = 5264.508| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.35 r_work: 0.3288 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2151 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= 0.118 Angle : 0.481 6.714 6812 Z= 0.255 Chirality : 0.043 0.130 696 Planarity : 0.003 0.027 890 Dihedral : 3.824 13.251 690 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.51 % Allowed : 16.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.32), residues: 606 helix: -4.77 (0.28), residues: 54 sheet: -0.69 (0.34), residues: 210 loop : -0.82 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 357 TYR 0.008 0.001 TYR D 495 PHE 0.029 0.001 PHE D 393 TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5008) covalent geometry : angle 0.48086 ( 6796) SS BOND : bond 0.00120 ( 8) SS BOND : angle 0.37614 ( 16) hydrogen bonds : bond 0.03083 ( 138) hydrogen bonds : angle 6.00410 ( 336) *********************** 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 91 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.219 Fit side-chains REVERT: B 386 LYS cc_start: 0.7792 (mmmt) cc_final: 0.7402 (mtmt) REVERT: A 39 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.6469 (tt0) REVERT: D 386 LYS cc_start: 0.7892 (mttt) cc_final: 0.7407 (mtpp) REVERT: D 484 GLU cc_start: 0.7103 (tm-30) cc_final: 0.6846 (tm-30) REVERT: C 27 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6543 (pp) REVERT: C 39 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7025 (tt0) REVERT: C 108 ARG cc_start: 0.7621 (mtm-85) cc_final: 0.7227 (mtt180) outliers start: 13 outliers final: 8 residues processed: 89 average time/residue: 0.1064 time to fit residues: 11.4248 Evaluate side-chains 87 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.156312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.127546 restraints weight = 5319.841| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.36 r_work: 0.3266 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2169 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= 0.160 Angle : 0.512 6.687 6812 Z= 0.271 Chirality : 0.044 0.131 696 Planarity : 0.003 0.028 890 Dihedral : 3.971 14.116 690 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.51 % Allowed : 16.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.32), residues: 606 helix: -4.75 (0.30), residues: 54 sheet: -0.69 (0.33), residues: 210 loop : -0.84 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 357 TYR 0.009 0.001 TYR B 489 PHE 0.028 0.001 PHE D 393 TRP 0.011 0.002 TRP D 353 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 5008) covalent geometry : angle 0.51183 ( 6796) SS BOND : bond 0.00165 ( 8) SS BOND : angle 0.43421 ( 16) hydrogen bonds : bond 0.03253 ( 138) hydrogen bonds : angle 6.10078 ( 336) ********************** 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 90 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.190 Fit side-chains REVERT: B 386 LYS cc_start: 0.7804 (mmmt) cc_final: 0.7409 (mtmt) REVERT: A 39 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.6523 (tt0) REVERT: D 386 LYS cc_start: 0.7910 (mttt) cc_final: 0.7415 (mtpp) REVERT: D 484 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6811 (tm-30) REVERT: C 27 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6588 (pp) REVERT: C 39 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.6926 (tt0) outliers start: 13 outliers final: 8 residues processed: 87 average time/residue: 0.1125 time to fit residues: 11.7931 Evaluate side-chains 87 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 0.0670 chunk 33 optimal weight: 0.0970 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.154464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.127947 restraints weight = 5272.853| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.18 r_work: 0.3275 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2192 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= 0.172 Angle : 0.522 6.651 6812 Z= 0.276 Chirality : 0.045 0.131 696 Planarity : 0.003 0.028 890 Dihedral : 4.078 14.588 690 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.70 % Allowed : 16.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.32), residues: 606 helix: -4.73 (0.32), residues: 54 sheet: -0.69 (0.33), residues: 210 loop : -0.84 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 357 TYR 0.011 0.001 TYR D 495 PHE 0.028 0.001 PHE D 393 TRP 0.011 0.002 TRP D 353 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 5008) covalent geometry : angle 0.52227 ( 6796) SS BOND : bond 0.00194 ( 8) SS BOND : angle 0.45013 ( 16) hydrogen bonds : bond 0.03337 ( 138) hydrogen bonds : angle 6.14537 ( 336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1652.26 seconds wall clock time: 29 minutes 1.89 seconds (1741.89 seconds total)