Starting phenix.real_space_refine on Tue Mar 3 16:40:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nf4_9360/03_2026/6nf4_9360.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nf4_9360/03_2026/6nf4_9360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nf4_9360/03_2026/6nf4_9360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nf4_9360/03_2026/6nf4_9360.map" model { file = "/net/cci-nas-00/data/ceres_data/6nf4_9360/03_2026/6nf4_9360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nf4_9360/03_2026/6nf4_9360.cif" } resolution = 2.98 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= 1.000 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 66 5.16 5 C 4630 2.51 5 N 1084 2.21 5 O 1180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6960 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3347 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 13, 'TRANS': 407} Chain breaks: 4 Chain: "B" Number of atoms: 3347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3347 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 13, 'TRANS': 407} Chain breaks: 4 Chain: "A" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 133 Unusual residues: {'CLR': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 133 Unusual residues: {'CLR': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.70, per 1000 atoms: 0.24 Number of scatterers: 6960 At special positions: 0 Unit cell: (85.49, 77.25, 72.1, 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 66 16.00 O 1180 8.00 N 1084 7.00 C 4630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 171.6 milliseconds 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 85.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 48 through 76 removed outlier: 3.517A pdb=" N ALA A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 109 removed outlier: 3.648A pdb=" N LEU A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 150 Processing helix chain 'A' and resid 158 through 181 Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 190 through 213 Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 249 through 283 Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 304 through 330 Processing helix chain 'A' and resid 334 through 367 removed outlier: 3.674A pdb=" N ALA A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 409 removed outlier: 3.571A pdb=" N THR A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLY A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 442 removed outlier: 3.707A pdb=" N TYR A 442 " --> pdb=" O VAL A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 537 Proline residue: A 535 - end of helix Processing helix chain 'A' and resid 540 through 545 removed outlier: 4.025A pdb=" N TYR A 543 " --> pdb=" O ARG A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 584 Proline residue: A 566 - end of helix Processing helix chain 'B' and resid 48 through 76 removed outlier: 3.517A pdb=" N ALA B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 109 removed outlier: 3.648A pdb=" N LEU B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 150 Processing helix chain 'B' and resid 158 through 181 Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 190 through 213 Processing helix chain 'B' and resid 215 through 220 Processing helix chain 'B' and resid 249 through 283 Proline residue: B 263 - end of helix Processing helix chain 'B' and resid 304 through 330 Processing helix chain 'B' and resid 334 through 367 removed outlier: 3.674A pdb=" N ALA B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.571A pdb=" N THR B 380 " --> pdb=" O ASN B 376 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLY B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER B 393 " --> pdb=" O SER B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 442 removed outlier: 3.707A pdb=" N TYR B 442 " --> pdb=" O VAL B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 537 Proline residue: B 535 - end of helix Processing helix chain 'B' and resid 540 through 545 removed outlier: 4.025A pdb=" N TYR B 543 " --> pdb=" O ARG B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 584 Proline residue: B 566 - end of helix 568 hydrogen bonds defined for protein. 1692 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: 1.07 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1170 1.33 - 1.45: 1864 1.45 - 1.57: 4006 1.57 - 1.69: 2 1.69 - 1.81: 110 Bond restraints: 7152 Sorted by residual: bond pdb=" CAX Y01 A 601 " pdb=" OAH Y01 A 601 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" CAX Y01 B 601 " pdb=" OAH Y01 B 601 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" CAX Y01 B 604 " pdb=" OAH Y01 B 604 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" CAX Y01 A 603 " pdb=" OAH Y01 A 603 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" CAX Y01 A 604 " pdb=" OAH Y01 A 604 " ideal model delta sigma weight residual 1.248 1.341 -0.093 2.00e-02 2.50e+03 2.17e+01 ... (remaining 7147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 9028 1.85 - 3.71: 552 3.71 - 5.56: 108 5.56 - 7.41: 44 7.41 - 9.26: 8 Bond angle restraints: 9740 Sorted by residual: angle pdb=" CA GLU A 550 " pdb=" CB GLU A 550 " pdb=" CG GLU A 550 " ideal model delta sigma weight residual 114.10 121.52 -7.42 2.00e+00 2.50e-01 1.38e+01 angle pdb=" CA GLU B 550 " pdb=" CB GLU B 550 " pdb=" CG GLU B 550 " ideal model delta sigma weight residual 114.10 121.52 -7.42 2.00e+00 2.50e-01 1.38e+01 angle pdb=" C ILE A 186 " pdb=" N LYS A 187 " pdb=" CA LYS A 187 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.29e+01 angle pdb=" C ILE B 186 " pdb=" N LYS B 187 " pdb=" CA LYS B 187 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.29e+01 angle pdb=" C ARG A 540 " pdb=" CA ARG A 540 " pdb=" CB ARG A 540 " ideal model delta sigma weight residual 111.20 108.80 2.40 7.10e-01 1.98e+00 1.14e+01 ... (remaining 9735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4202 17.88 - 35.75: 274 35.75 - 53.63: 60 53.63 - 71.51: 12 71.51 - 89.38: 10 Dihedral angle restraints: 4558 sinusoidal: 2102 harmonic: 2456 Sorted by residual: dihedral pdb=" CA GLU A 548 " pdb=" C GLU A 548 " pdb=" N ASN A 549 " pdb=" CA ASN A 549 " ideal model delta harmonic sigma weight residual 180.00 154.91 25.09 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA GLU B 548 " pdb=" C GLU B 548 " pdb=" N ASN B 549 " pdb=" CA ASN B 549 " ideal model delta harmonic sigma weight residual 180.00 154.91 25.09 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA MET A 371 " pdb=" C MET A 371 " pdb=" N ASP A 372 " pdb=" CA ASP A 372 " ideal model delta harmonic sigma weight residual 180.00 155.89 24.11 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 4555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 946 0.077 - 0.153: 148 0.153 - 0.230: 18 0.230 - 0.307: 14 0.307 - 0.383: 8 Chirality restraints: 1134 Sorted by residual: chirality pdb=" CBG Y01 B 604 " pdb=" CAQ Y01 B 604 " pdb=" CBD Y01 B 604 " pdb=" CBI Y01 B 604 " both_signs ideal model delta sigma weight residual False -2.33 -2.72 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CBG Y01 A 603 " pdb=" CAQ Y01 A 603 " pdb=" CBD Y01 A 603 " pdb=" CBI Y01 A 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.72 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CBG Y01 B 603 " pdb=" CAQ Y01 B 603 " pdb=" CBD Y01 B 603 " pdb=" CBI Y01 B 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.70 0.36 2.00e-01 2.50e+01 3.32e+00 ... (remaining 1131 not shown) Planarity restraints: 1134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 170 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C HIS B 170 " 0.066 2.00e-02 2.50e+03 pdb=" O HIS B 170 " -0.025 2.00e-02 2.50e+03 pdb=" N THR B 171 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 170 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C HIS A 170 " -0.066 2.00e-02 2.50e+03 pdb=" O HIS A 170 " 0.025 2.00e-02 2.50e+03 pdb=" N THR A 171 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 171 " 0.016 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C THR B 171 " -0.057 2.00e-02 2.50e+03 pdb=" O THR B 171 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE B 172 " 0.019 2.00e-02 2.50e+03 ... (remaining 1131 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 2448 2.88 - 3.39: 6908 3.39 - 3.89: 11691 3.89 - 4.40: 12724 4.40 - 4.90: 22596 Nonbonded interactions: 56367 Sorted by model distance: nonbonded pdb=" O ARG B 379 " pdb=" OG1 THR B 383 " model vdw 2.379 3.040 nonbonded pdb=" O ARG A 379 " pdb=" OG1 THR A 383 " model vdw 2.379 3.040 nonbonded pdb=" OG1 THR B 216 " pdb=" ND2 ASN B 562 " model vdw 2.393 3.120 nonbonded pdb=" OG1 THR A 216 " pdb=" ND2 ASN A 562 " model vdw 2.393 3.120 nonbonded pdb=" O GLN A 515 " pdb=" ND2 ASN A 519 " model vdw 2.408 3.120 ... (remaining 56362 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 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.000 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:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 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 : 0.009 0.094 7152 Z= 0.391 Angle : 1.092 9.263 9740 Z= 0.552 Chirality : 0.070 0.383 1134 Planarity : 0.007 0.043 1134 Dihedral : 13.593 89.384 2974 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.27 % Allowed : 1.63 % Favored : 98.10 % 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 are not related in a simple way. whole: 0.16 (0.27), residues: 822 helix: 0.66 (0.17), residues: 696 sheet: None (None), residues: 0 loop : -2.68 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 379 TYR 0.018 0.003 TYR B 189 PHE 0.025 0.003 PHE B 525 TRP 0.016 0.003 TRP A 417 HIS 0.006 0.001 HIS B 574 Details of bonding type rmsd covalent geometry : bond 0.00901 ( 7152) covalent geometry : angle 1.09187 ( 9740) hydrogen bonds : bond 0.11727 ( 568) hydrogen bonds : angle 5.08809 ( 1692) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 0.254 Fit side-chains REVERT: A 429 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7966 (pp20) REVERT: B 429 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7964 (pp20) outliers start: 2 outliers final: 0 residues processed: 148 average time/residue: 0.7129 time to fit residues: 109.7235 Evaluate side-chains 100 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN A 562 ASN B 433 GLN B 562 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.169752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.119014 restraints weight = 7174.066| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.27 r_work: 0.3179 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7152 Z= 0.134 Angle : 0.553 6.389 9740 Z= 0.290 Chirality : 0.038 0.155 1134 Planarity : 0.004 0.034 1134 Dihedral : 9.831 54.939 1460 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.71 % Allowed : 10.03 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.29), residues: 822 helix: 2.40 (0.18), residues: 700 sheet: None (None), residues: 0 loop : -2.47 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 128 TYR 0.011 0.001 TYR B 189 PHE 0.017 0.002 PHE B 525 TRP 0.010 0.001 TRP A 417 HIS 0.004 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7152) covalent geometry : angle 0.55325 ( 9740) hydrogen bonds : bond 0.04981 ( 568) hydrogen bonds : angle 3.58178 ( 1692) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.270 Fit side-chains REVERT: A 84 GLU cc_start: 0.8216 (pm20) cc_final: 0.7888 (mp0) REVERT: A 179 TRP cc_start: 0.8363 (OUTLIER) cc_final: 0.8027 (m100) REVERT: A 275 MET cc_start: 0.8384 (mtp) cc_final: 0.8093 (mtm) REVERT: A 350 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8187 (mtp) REVERT: A 364 TYR cc_start: 0.9043 (m-10) cc_final: 0.8694 (m-80) REVERT: A 443 ARG cc_start: 0.8216 (mtp85) cc_final: 0.7882 (mtm180) REVERT: B 84 GLU cc_start: 0.8232 (pm20) cc_final: 0.7899 (mp0) REVERT: B 179 TRP cc_start: 0.8365 (OUTLIER) cc_final: 0.8030 (m100) REVERT: B 275 MET cc_start: 0.8381 (mtp) cc_final: 0.8090 (mtm) REVERT: B 350 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8185 (mtp) REVERT: B 364 TYR cc_start: 0.9038 (m-10) cc_final: 0.8688 (m-80) REVERT: B 443 ARG cc_start: 0.8216 (mtp85) cc_final: 0.7881 (mtm180) outliers start: 20 outliers final: 4 residues processed: 126 average time/residue: 0.5540 time to fit residues: 73.3235 Evaluate side-chains 110 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 41 optimal weight: 0.0370 chunk 14 optimal weight: 0.6980 chunk 80 optimal weight: 0.1980 chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 433 GLN B 176 HIS B 433 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.168195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117886 restraints weight = 7269.045| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.27 r_work: 0.3212 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7152 Z= 0.116 Angle : 0.514 8.049 9740 Z= 0.264 Chirality : 0.037 0.144 1134 Planarity : 0.004 0.036 1134 Dihedral : 9.085 55.874 1460 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.79 % Allowed : 11.11 % Favored : 85.09 % 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 are not related in a simple way. whole: 3.53 (0.30), residues: 822 helix: 3.03 (0.18), residues: 710 sheet: None (None), residues: 0 loop : -2.85 (0.58), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 107 TYR 0.012 0.001 TYR A 442 PHE 0.015 0.001 PHE B 202 TRP 0.010 0.001 TRP B 280 HIS 0.002 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 7152) covalent geometry : angle 0.51448 ( 9740) hydrogen bonds : bond 0.04239 ( 568) hydrogen bonds : angle 3.24191 ( 1692) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.169 Fit side-chains REVERT: A 128 ARG cc_start: 0.7373 (mtm-85) cc_final: 0.7076 (mtt-85) REVERT: A 179 TRP cc_start: 0.8276 (OUTLIER) cc_final: 0.8022 (t60) REVERT: A 275 MET cc_start: 0.8319 (mtp) cc_final: 0.8024 (mtm) REVERT: A 362 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8148 (mp) REVERT: A 364 TYR cc_start: 0.8955 (m-10) cc_final: 0.8536 (m-80) REVERT: A 391 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8365 (mp) REVERT: A 443 ARG cc_start: 0.8192 (mtp85) cc_final: 0.7887 (mtm180) REVERT: B 128 ARG cc_start: 0.7384 (mtm-85) cc_final: 0.7087 (mtt-85) REVERT: B 179 TRP cc_start: 0.8282 (OUTLIER) cc_final: 0.8027 (t60) REVERT: B 275 MET cc_start: 0.8302 (mtp) cc_final: 0.8008 (mtm) REVERT: B 362 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8146 (mp) REVERT: B 364 TYR cc_start: 0.8954 (m-10) cc_final: 0.8534 (m-80) REVERT: B 391 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8372 (mp) REVERT: B 443 ARG cc_start: 0.8188 (mtp85) cc_final: 0.7883 (mtm180) outliers start: 28 outliers final: 8 residues processed: 128 average time/residue: 0.5798 time to fit residues: 77.8199 Evaluate side-chains 120 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 0.0020 chunk 69 optimal weight: 30.0000 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN B 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.168022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117624 restraints weight = 7311.048| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.29 r_work: 0.3212 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7152 Z= 0.116 Angle : 0.516 8.580 9740 Z= 0.260 Chirality : 0.037 0.150 1134 Planarity : 0.004 0.038 1134 Dihedral : 8.570 56.782 1460 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.52 % Allowed : 12.74 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.93 (0.30), residues: 822 helix: 3.36 (0.18), residues: 706 sheet: None (None), residues: 0 loop : -2.97 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 107 TYR 0.008 0.001 TYR B 189 PHE 0.016 0.001 PHE A 202 TRP 0.011 0.001 TRP B 280 HIS 0.002 0.001 HIS A 574 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 7152) covalent geometry : angle 0.51560 ( 9740) hydrogen bonds : bond 0.04046 ( 568) hydrogen bonds : angle 3.08995 ( 1692) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.251 Fit side-chains REVERT: A 128 ARG cc_start: 0.7370 (mtm-85) cc_final: 0.7060 (mtt-85) REVERT: A 179 TRP cc_start: 0.8303 (OUTLIER) cc_final: 0.8045 (t60) REVERT: A 364 TYR cc_start: 0.8960 (m-10) cc_final: 0.8587 (m-80) REVERT: A 391 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8401 (mp) REVERT: A 443 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7820 (mtm180) REVERT: B 128 ARG cc_start: 0.7379 (mtm-85) cc_final: 0.7075 (mtt-85) REVERT: B 179 TRP cc_start: 0.8305 (OUTLIER) cc_final: 0.8051 (t60) REVERT: B 364 TYR cc_start: 0.8952 (m-10) cc_final: 0.8576 (m-80) REVERT: B 391 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8405 (mp) REVERT: B 443 ARG cc_start: 0.8167 (mtp85) cc_final: 0.7823 (mtm180) outliers start: 26 outliers final: 4 residues processed: 126 average time/residue: 0.6025 time to fit residues: 79.5247 Evaluate side-chains 116 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN A 410 GLN A 433 GLN A 519 ASN B 174 GLN B 410 GLN B 433 GLN B 519 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.162237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111787 restraints weight = 7312.270| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.25 r_work: 0.3119 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7152 Z= 0.209 Angle : 0.596 10.132 9740 Z= 0.294 Chirality : 0.041 0.155 1134 Planarity : 0.004 0.039 1134 Dihedral : 8.378 53.542 1460 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.98 % Allowed : 15.72 % Favored : 81.30 % 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 are not related in a simple way. whole: 3.64 (0.30), residues: 822 helix: 3.14 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -3.18 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 107 TYR 0.010 0.001 TYR A 343 PHE 0.018 0.002 PHE B 525 TRP 0.010 0.001 TRP A 280 HIS 0.004 0.001 HIS B 574 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 7152) covalent geometry : angle 0.59593 ( 9740) hydrogen bonds : bond 0.04927 ( 568) hydrogen bonds : angle 3.20066 ( 1692) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.235 Fit side-chains REVERT: A 84 GLU cc_start: 0.8303 (mp0) cc_final: 0.8010 (mp0) REVERT: A 128 ARG cc_start: 0.7580 (mtm-85) cc_final: 0.7209 (mtt-85) REVERT: A 179 TRP cc_start: 0.8377 (OUTLIER) cc_final: 0.8164 (t60) REVERT: A 336 GLU cc_start: 0.6225 (pm20) cc_final: 0.5848 (mm-30) REVERT: A 364 TYR cc_start: 0.9011 (m-10) cc_final: 0.8706 (m-80) REVERT: A 443 ARG cc_start: 0.8220 (mtp85) cc_final: 0.8008 (mtm180) REVERT: B 84 GLU cc_start: 0.8314 (mp0) cc_final: 0.8024 (mp0) REVERT: B 128 ARG cc_start: 0.7585 (mtm-85) cc_final: 0.7210 (mtt-85) REVERT: B 179 TRP cc_start: 0.8384 (OUTLIER) cc_final: 0.8172 (t60) REVERT: B 336 GLU cc_start: 0.6216 (pm20) cc_final: 0.5858 (mm-30) REVERT: B 364 TYR cc_start: 0.9011 (m-10) cc_final: 0.8706 (m-80) REVERT: B 443 ARG cc_start: 0.8213 (mtp85) cc_final: 0.8001 (mtm180) outliers start: 22 outliers final: 6 residues processed: 122 average time/residue: 0.6109 time to fit residues: 77.9888 Evaluate side-chains 116 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 46 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 0.0870 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 13 optimal weight: 5.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN B 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.166779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.116619 restraints weight = 7337.692| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.30 r_work: 0.3198 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7152 Z= 0.112 Angle : 0.531 8.845 9740 Z= 0.267 Chirality : 0.037 0.165 1134 Planarity : 0.004 0.038 1134 Dihedral : 8.100 55.242 1460 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.25 % Allowed : 15.45 % Favored : 81.30 % 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 are not related in a simple way. whole: 4.04 (0.30), residues: 822 helix: 3.48 (0.19), residues: 706 sheet: None (None), residues: 0 loop : -3.21 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 514 TYR 0.008 0.001 TYR A 189 PHE 0.015 0.001 PHE B 525 TRP 0.008 0.001 TRP B 417 HIS 0.002 0.000 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 7152) covalent geometry : angle 0.53134 ( 9740) hydrogen bonds : bond 0.03953 ( 568) hydrogen bonds : angle 3.06191 ( 1692) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.271 Fit side-chains REVERT: A 84 GLU cc_start: 0.8179 (mp0) cc_final: 0.7933 (mp0) REVERT: A 128 ARG cc_start: 0.7367 (mtm-85) cc_final: 0.7072 (mtt-85) REVERT: A 179 TRP cc_start: 0.8240 (OUTLIER) cc_final: 0.7981 (t60) REVERT: A 336 GLU cc_start: 0.6075 (pm20) cc_final: 0.5659 (mm-30) REVERT: A 364 TYR cc_start: 0.8974 (m-10) cc_final: 0.8654 (m-80) REVERT: A 391 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8452 (mp) REVERT: A 443 ARG cc_start: 0.8167 (mtp85) cc_final: 0.7837 (mtm180) REVERT: B 84 GLU cc_start: 0.8188 (mp0) cc_final: 0.7944 (mp0) REVERT: B 128 ARG cc_start: 0.7364 (mtm-85) cc_final: 0.7072 (mtt-85) REVERT: B 179 TRP cc_start: 0.8244 (OUTLIER) cc_final: 0.7980 (t60) REVERT: B 336 GLU cc_start: 0.6064 (pm20) cc_final: 0.5662 (mm-30) REVERT: B 364 TYR cc_start: 0.8975 (m-10) cc_final: 0.8657 (m-80) REVERT: B 391 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8456 (mp) REVERT: B 443 ARG cc_start: 0.8164 (mtp85) cc_final: 0.7831 (mtm180) outliers start: 24 outliers final: 8 residues processed: 126 average time/residue: 0.6329 time to fit residues: 83.5597 Evaluate side-chains 126 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 57 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 65 optimal weight: 0.0020 chunk 0 optimal weight: 7.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN A 433 GLN B 174 GLN B 433 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.166742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.116977 restraints weight = 7288.569| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.27 r_work: 0.3200 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7152 Z= 0.113 Angle : 0.497 8.503 9740 Z= 0.248 Chirality : 0.037 0.162 1134 Planarity : 0.004 0.039 1134 Dihedral : 7.797 55.542 1460 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.52 % Allowed : 14.63 % Favored : 81.84 % 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 are not related in a simple way. whole: 4.24 (0.30), residues: 822 helix: 3.70 (0.18), residues: 694 sheet: None (None), residues: 0 loop : -3.00 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 514 TYR 0.011 0.001 TYR A 442 PHE 0.016 0.001 PHE A 202 TRP 0.007 0.001 TRP B 179 HIS 0.002 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 7152) covalent geometry : angle 0.49700 ( 9740) hydrogen bonds : bond 0.03933 ( 568) hydrogen bonds : angle 3.00218 ( 1692) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.250 Fit side-chains REVERT: A 84 GLU cc_start: 0.8246 (mp0) cc_final: 0.7969 (mp0) REVERT: A 128 ARG cc_start: 0.7334 (mtm-85) cc_final: 0.7098 (mtm-85) REVERT: A 179 TRP cc_start: 0.8189 (OUTLIER) cc_final: 0.7952 (t60) REVERT: A 336 GLU cc_start: 0.6131 (pm20) cc_final: 0.5766 (mm-30) REVERT: A 341 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7913 (ttp) REVERT: A 364 TYR cc_start: 0.8955 (m-10) cc_final: 0.8655 (m-80) REVERT: A 391 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8426 (mp) REVERT: A 443 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7819 (mtm180) REVERT: B 84 GLU cc_start: 0.8254 (mp0) cc_final: 0.7976 (mp0) REVERT: B 128 ARG cc_start: 0.7330 (mtm-85) cc_final: 0.7096 (mtm-85) REVERT: B 179 TRP cc_start: 0.8191 (OUTLIER) cc_final: 0.7953 (t60) REVERT: B 336 GLU cc_start: 0.6111 (pm20) cc_final: 0.5755 (mm-30) REVERT: B 341 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7901 (ttp) REVERT: B 364 TYR cc_start: 0.8959 (m-10) cc_final: 0.8662 (m-80) REVERT: B 391 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8429 (mp) REVERT: B 443 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7815 (mtm180) outliers start: 26 outliers final: 4 residues processed: 130 average time/residue: 0.6370 time to fit residues: 86.6982 Evaluate side-chains 124 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 72 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN A 433 GLN B 174 GLN B 433 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.167162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117185 restraints weight = 7370.546| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.28 r_work: 0.3200 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7152 Z= 0.118 Angle : 0.498 8.685 9740 Z= 0.248 Chirality : 0.037 0.163 1134 Planarity : 0.004 0.039 1134 Dihedral : 7.604 56.240 1460 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.44 % Allowed : 15.99 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.24 (0.30), residues: 822 helix: 3.68 (0.18), residues: 696 sheet: None (None), residues: 0 loop : -2.99 (0.54), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 514 TYR 0.009 0.001 TYR B 344 PHE 0.015 0.001 PHE A 525 TRP 0.007 0.001 TRP B 179 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 7152) covalent geometry : angle 0.49812 ( 9740) hydrogen bonds : bond 0.03903 ( 568) hydrogen bonds : angle 2.96757 ( 1692) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.215 Fit side-chains REVERT: A 84 GLU cc_start: 0.8251 (mp0) cc_final: 0.7977 (mp0) REVERT: A 128 ARG cc_start: 0.7359 (mtm-85) cc_final: 0.7125 (mtm-85) REVERT: A 179 TRP cc_start: 0.8248 (OUTLIER) cc_final: 0.8023 (t60) REVERT: A 336 GLU cc_start: 0.6184 (pm20) cc_final: 0.5843 (mm-30) REVERT: A 341 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7938 (ttp) REVERT: A 364 TYR cc_start: 0.8943 (m-10) cc_final: 0.8720 (m-80) REVERT: A 391 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8425 (mp) REVERT: A 443 ARG cc_start: 0.8122 (mtp85) cc_final: 0.7793 (mtm180) REVERT: B 84 GLU cc_start: 0.8259 (mp0) cc_final: 0.7986 (mp0) REVERT: B 128 ARG cc_start: 0.7355 (mtm-85) cc_final: 0.7123 (mtm-85) REVERT: B 179 TRP cc_start: 0.8250 (OUTLIER) cc_final: 0.8021 (t60) REVERT: B 336 GLU cc_start: 0.6173 (pm20) cc_final: 0.5836 (mm-30) REVERT: B 341 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7934 (ttp) REVERT: B 364 TYR cc_start: 0.8944 (m-10) cc_final: 0.8723 (m-80) REVERT: B 391 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8426 (mp) REVERT: B 443 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7784 (mtm180) outliers start: 18 outliers final: 6 residues processed: 130 average time/residue: 0.6082 time to fit residues: 83.0139 Evaluate side-chains 128 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 530 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 53 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN A 433 GLN A 519 ASN B 174 GLN B 433 GLN B 519 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.165285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115334 restraints weight = 7280.071| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.27 r_work: 0.3172 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7152 Z= 0.155 Angle : 0.529 9.230 9740 Z= 0.263 Chirality : 0.039 0.173 1134 Planarity : 0.004 0.040 1134 Dihedral : 7.625 55.465 1460 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.71 % Allowed : 15.72 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.02 (0.30), residues: 822 helix: 3.52 (0.18), residues: 698 sheet: None (None), residues: 0 loop : -3.12 (0.53), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 514 TYR 0.011 0.001 TYR B 442 PHE 0.016 0.002 PHE A 525 TRP 0.007 0.001 TRP B 179 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7152) covalent geometry : angle 0.52930 ( 9740) hydrogen bonds : bond 0.04276 ( 568) hydrogen bonds : angle 3.04474 ( 1692) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.254 Fit side-chains REVERT: A 84 GLU cc_start: 0.8264 (mp0) cc_final: 0.7986 (mp0) REVERT: A 128 ARG cc_start: 0.7440 (mtm-85) cc_final: 0.7153 (mtm-85) REVERT: A 179 TRP cc_start: 0.8290 (OUTLIER) cc_final: 0.8040 (t60) REVERT: A 336 GLU cc_start: 0.6211 (pm20) cc_final: 0.5877 (mm-30) REVERT: A 341 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.8040 (ttp) REVERT: A 364 TYR cc_start: 0.8982 (m-10) cc_final: 0.8747 (m-80) REVERT: A 391 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8451 (mp) REVERT: A 443 ARG cc_start: 0.8189 (mtp85) cc_final: 0.7843 (mtm180) REVERT: B 84 GLU cc_start: 0.8280 (mp0) cc_final: 0.8001 (mp0) REVERT: B 128 ARG cc_start: 0.7447 (mtm-85) cc_final: 0.7163 (mtm-85) REVERT: B 179 TRP cc_start: 0.8290 (OUTLIER) cc_final: 0.8042 (t60) REVERT: B 336 GLU cc_start: 0.6194 (pm20) cc_final: 0.5867 (mm-30) REVERT: B 341 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.8038 (ttp) REVERT: B 364 TYR cc_start: 0.8983 (m-10) cc_final: 0.8746 (m-80) REVERT: B 391 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8454 (mp) REVERT: B 443 ARG cc_start: 0.8181 (mtp85) cc_final: 0.7832 (mtm180) outliers start: 20 outliers final: 8 residues processed: 134 average time/residue: 0.5878 time to fit residues: 82.7865 Evaluate side-chains 136 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 530 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 3 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN A 433 GLN ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN B 433 GLN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.166998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.116549 restraints weight = 7272.010| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.30 r_work: 0.3192 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7152 Z= 0.126 Angle : 0.511 8.921 9740 Z= 0.257 Chirality : 0.038 0.170 1134 Planarity : 0.004 0.039 1134 Dihedral : 7.582 56.489 1460 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.98 % Allowed : 15.18 % Favored : 81.84 % 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 are not related in a simple way. whole: 4.09 (0.30), residues: 822 helix: 3.56 (0.18), residues: 696 sheet: None (None), residues: 0 loop : -2.90 (0.54), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 514 TYR 0.011 0.001 TYR B 344 PHE 0.016 0.001 PHE B 525 TRP 0.006 0.001 TRP B 179 HIS 0.002 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7152) covalent geometry : angle 0.51139 ( 9740) hydrogen bonds : bond 0.04041 ( 568) hydrogen bonds : angle 3.04042 ( 1692) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.261 Fit side-chains REVERT: A 84 GLU cc_start: 0.8245 (mp0) cc_final: 0.8007 (mp0) REVERT: A 128 ARG cc_start: 0.7413 (mtm-85) cc_final: 0.7159 (mtm-85) REVERT: A 179 TRP cc_start: 0.8279 (OUTLIER) cc_final: 0.7992 (t60) REVERT: A 336 GLU cc_start: 0.6190 (pm20) cc_final: 0.5862 (mm-30) REVERT: A 341 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.8042 (ttp) REVERT: A 364 TYR cc_start: 0.8960 (m-10) cc_final: 0.8722 (m-80) REVERT: A 391 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8462 (mp) REVERT: A 443 ARG cc_start: 0.8206 (mtp85) cc_final: 0.7861 (mtm180) REVERT: B 84 GLU cc_start: 0.8257 (mp0) cc_final: 0.8019 (mp0) REVERT: B 128 ARG cc_start: 0.7418 (mtm-85) cc_final: 0.7165 (mtm-85) REVERT: B 179 TRP cc_start: 0.8280 (OUTLIER) cc_final: 0.7999 (t60) REVERT: B 336 GLU cc_start: 0.6179 (pm20) cc_final: 0.5855 (mm-30) REVERT: B 341 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8042 (ttp) REVERT: B 364 TYR cc_start: 0.8962 (m-10) cc_final: 0.8725 (m-80) REVERT: B 391 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8466 (mp) REVERT: B 443 ARG cc_start: 0.8206 (mtp85) cc_final: 0.7862 (mtm180) outliers start: 22 outliers final: 8 residues processed: 134 average time/residue: 0.5874 time to fit residues: 82.5025 Evaluate side-chains 136 residues out of total 738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 530 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN A 433 GLN A 562 ASN B 174 GLN B 433 GLN B 562 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.167860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117725 restraints weight = 7265.389| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.29 r_work: 0.3213 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7152 Z= 0.118 Angle : 0.503 8.715 9740 Z= 0.255 Chirality : 0.037 0.172 1134 Planarity : 0.004 0.039 1134 Dihedral : 7.501 58.262 1460 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.71 % Allowed : 15.45 % Favored : 81.84 % 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 are not related in a simple way. whole: 4.13 (0.30), residues: 822 helix: 3.58 (0.18), residues: 696 sheet: None (None), residues: 0 loop : -2.90 (0.54), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 514 TYR 0.016 0.001 TYR B 442 PHE 0.015 0.001 PHE A 202 TRP 0.006 0.001 TRP B 100 HIS 0.002 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7152) covalent geometry : angle 0.50334 ( 9740) hydrogen bonds : bond 0.03910 ( 568) hydrogen bonds : angle 3.02833 ( 1692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2246.29 seconds wall clock time: 39 minutes 3.02 seconds (2343.02 seconds total)