Starting phenix.real_space_refine on Tue Feb 3 14:17:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x45_66530/02_2026/9x45_66530.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x45_66530/02_2026/9x45_66530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x45_66530/02_2026/9x45_66530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x45_66530/02_2026/9x45_66530.map" model { file = "/net/cci-nas-00/data/ceres_data/9x45_66530/02_2026/9x45_66530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x45_66530/02_2026/9x45_66530.cif" } resolution = 2.93 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= 0.001 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 12 5.16 5 C 2202 2.51 5 N 636 2.21 5 O 738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3588 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 598 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 0.63, per 1000 atoms: 0.18 Number of scatterers: 3588 At special positions: 0 Unit cell: (157.17, 72.54, 34.41, 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 12 16.00 O 738 8.00 N 636 7.00 C 2202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " 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: 0.28 Conformation dependent library (CDL) restraints added in 153.2 milliseconds 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 876 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.060A pdb=" N THR A 19 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR B 19 " --> pdb=" O ILE C 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 28 Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 77 Processing sheet with id=AA5, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA6, first strand: chain 'D' and resid 19 through 21 removed outlier: 6.087A pdb=" N THR D 19 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N THR E 19 " --> pdb=" O ILE F 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 27 through 28 Processing sheet with id=AA8, first strand: chain 'D' and resid 49 through 51 Processing sheet with id=AA9, first strand: chain 'D' and resid 76 through 77 17 hydrogen bonds defined for protein. 51 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: 0.42 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1212 1.34 - 1.46: 838 1.46 - 1.58: 1610 1.58 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 3672 Sorted by residual: bond pdb=" CB ASP E 83 " pdb=" CG ASP E 83 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.55e-01 bond pdb=" CB ASP D 83 " pdb=" CG ASP D 83 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.24e-01 bond pdb=" CB ASP B 83 " pdb=" CG ASP B 83 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 6.88e-01 bond pdb=" CB ASP F 83 " pdb=" CG ASP F 83 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 6.79e-01 bond pdb=" CB ASP A 83 " pdb=" CG ASP A 83 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.50e-01 ... (remaining 3667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 4482 1.08 - 2.17: 398 2.17 - 3.25: 65 3.25 - 4.34: 35 4.34 - 5.42: 18 Bond angle restraints: 4998 Sorted by residual: angle pdb=" N ASP D 83 " pdb=" CA ASP D 83 " pdb=" C ASP D 83 " ideal model delta sigma weight residual 110.44 105.96 4.48 1.20e+00 6.94e-01 1.40e+01 angle pdb=" N ASP C 83 " pdb=" CA ASP C 83 " pdb=" C ASP C 83 " ideal model delta sigma weight residual 110.44 105.98 4.46 1.20e+00 6.94e-01 1.38e+01 angle pdb=" N ASP A 83 " pdb=" CA ASP A 83 " pdb=" C ASP A 83 " ideal model delta sigma weight residual 110.44 105.99 4.45 1.20e+00 6.94e-01 1.38e+01 angle pdb=" N ASP F 83 " pdb=" CA ASP F 83 " pdb=" C ASP F 83 " ideal model delta sigma weight residual 110.44 106.01 4.43 1.20e+00 6.94e-01 1.36e+01 angle pdb=" N ASP E 83 " pdb=" CA ASP E 83 " pdb=" C ASP E 83 " ideal model delta sigma weight residual 110.44 106.02 4.42 1.20e+00 6.94e-01 1.36e+01 ... (remaining 4993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.99: 1644 10.99 - 21.99: 264 21.99 - 32.98: 162 32.98 - 43.97: 66 43.97 - 54.96: 36 Dihedral angle restraints: 2172 sinusoidal: 804 harmonic: 1368 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 89 " pdb=" CB CYS B 89 " ideal model delta sinusoidal sigma weight residual -86.00 -123.63 37.63 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 89 " pdb=" CB CYS A 89 " ideal model delta sinusoidal sigma weight residual -86.00 -123.59 37.59 1 1.00e+01 1.00e-02 1.99e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 89 " pdb=" CB CYS D 89 " ideal model delta sinusoidal sigma weight residual -86.00 -123.59 37.59 1 1.00e+01 1.00e-02 1.99e+01 ... (remaining 2169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 293 0.030 - 0.059: 163 0.059 - 0.088: 54 0.088 - 0.118: 24 0.118 - 0.147: 6 Chirality restraints: 540 Sorted by residual: chirality pdb=" CA TRP D 36 " pdb=" N TRP D 36 " pdb=" C TRP D 36 " pdb=" CB TRP D 36 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA TRP A 36 " pdb=" N TRP A 36 " pdb=" C TRP A 36 " pdb=" CB TRP A 36 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA TRP E 36 " pdb=" N TRP E 36 " pdb=" C TRP E 36 " pdb=" CB TRP E 36 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 537 not shown) Planarity restraints: 660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 83 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C ASP B 83 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP B 83 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU B 84 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 83 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" C ASP A 83 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP A 83 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU A 84 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 83 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.78e+00 pdb=" C ASP D 83 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP D 83 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU D 84 " 0.011 2.00e-02 2.50e+03 ... (remaining 657 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 351 2.74 - 3.28: 3715 3.28 - 3.82: 5807 3.82 - 4.36: 6660 4.36 - 4.90: 13053 Nonbonded interactions: 29586 Sorted by model distance: nonbonded pdb=" O GLY D 30 " pdb=" ND2 ASN E 32 " model vdw 2.196 3.120 nonbonded pdb=" O GLY E 30 " pdb=" ND2 ASN F 32 " model vdw 2.242 3.120 nonbonded pdb=" O GLY A 30 " pdb=" ND2 ASN B 32 " model vdw 2.249 3.120 nonbonded pdb=" O GLY B 30 " pdb=" ND2 ASN C 32 " model vdw 2.329 3.120 nonbonded pdb=" ND2 ASN B 53 " pdb=" O ASN C 52 " model vdw 2.348 3.120 ... (remaining 29581 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 7.350 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: 0.010 Set scattering table: 0.010 Process input model: 5.130 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 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 : 0.003 0.022 3678 Z= 0.151 Angle : 0.749 5.421 5010 Z= 0.426 Chirality : 0.044 0.147 540 Planarity : 0.005 0.036 660 Dihedral : 17.026 54.964 1278 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.92 % Favored : 73.08 % Rotamer: Outliers : 0.00 % Allowed : 31.82 % Favored : 68.18 % 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: -5.84 (0.26), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.45 (0.20), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 62 TYR 0.006 0.001 TYR E 50 PHE 0.020 0.003 PHE F 37 TRP 0.002 0.001 TRP D 36 HIS 0.002 0.001 HIS F 86 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3672) covalent geometry : angle 0.74960 ( 4998) SS BOND : bond 0.00048 ( 6) SS BOND : angle 0.35721 ( 12) hydrogen bonds : bond 0.25725 ( 17) hydrogen bonds : angle 10.73084 ( 51) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.130 Fit side-chains REVERT: C 88 TYR cc_start: 0.7486 (m-80) cc_final: 0.7284 (m-80) REVERT: D 88 TYR cc_start: 0.7116 (m-80) cc_final: 0.6627 (m-80) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.3900 time to fit residues: 25.4972 Evaluate side-chains 40 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 HIS B 28 ASN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS C 28 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS D 28 ASN E 28 ASN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN F 28 ASN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.178566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.168881 restraints weight = 5224.936| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 2.19 r_work: 0.4265 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4168 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.067 3678 Z= 0.436 Angle : 1.233 11.248 5010 Z= 0.668 Chirality : 0.065 0.276 540 Planarity : 0.009 0.050 660 Dihedral : 9.688 31.847 510 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.64 % Allowed : 28.85 % Favored : 70.51 % Rotamer: Outliers : 11.11 % Allowed : 34.09 % Favored : 54.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.89 % 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: -6.21 (0.23), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.73 (0.17), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 62 TYR 0.022 0.004 TYR E 88 PHE 0.034 0.007 PHE E 37 TRP 0.041 0.009 TRP D 92 HIS 0.005 0.002 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00974 ( 3672) covalent geometry : angle 1.23315 ( 4998) SS BOND : bond 0.00727 ( 6) SS BOND : angle 1.22644 ( 12) hydrogen bonds : bond 0.05504 ( 17) hydrogen bonds : angle 6.90748 ( 51) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 30 time to evaluate : 0.080 Fit side-chains REVERT: A 67 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7959 (tmtp) REVERT: A 83 ASP cc_start: 0.6952 (t0) cc_final: 0.6688 (t0) REVERT: A 87 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.6226 (t80) REVERT: B 87 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6002 (t80) REVERT: C 83 ASP cc_start: 0.6784 (t0) cc_final: 0.6528 (t0) REVERT: C 87 TYR cc_start: 0.7120 (OUTLIER) cc_final: 0.5904 (t80) REVERT: D 17 ARG cc_start: 0.6460 (ptm160) cc_final: 0.5730 (mmm160) REVERT: D 67 LYS cc_start: 0.8224 (tttm) cc_final: 0.8010 (tmtt) REVERT: D 83 ASP cc_start: 0.7039 (t0) cc_final: 0.6754 (t0) REVERT: E 53 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7764 (m-40) outliers start: 44 outliers final: 17 residues processed: 73 average time/residue: 0.2405 time to fit residues: 18.4972 Evaluate side-chains 49 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 27 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 87 TYR Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain F residue 39 HIS Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 79 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.199858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.188915 restraints weight = 5163.705| |-----------------------------------------------------------------------------| r_work (start): 0.4575 rms_B_bonded: 2.44 r_work: 0.4496 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.4398 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.4398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3678 Z= 0.143 Angle : 0.812 8.619 5010 Z= 0.427 Chirality : 0.047 0.168 540 Planarity : 0.006 0.041 660 Dihedral : 7.613 23.314 510 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.85 % Favored : 74.15 % Rotamer: Outliers : 6.31 % Allowed : 33.84 % Favored : 59.85 % 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: -5.86 (0.24), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.46 (0.18), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 55 TYR 0.014 0.002 TYR B 50 PHE 0.013 0.002 PHE E 37 TRP 0.010 0.002 TRP C 36 HIS 0.008 0.001 HIS B 39 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 3672) covalent geometry : angle 0.81313 ( 4998) SS BOND : bond 0.00033 ( 6) SS BOND : angle 0.41870 ( 12) hydrogen bonds : bond 0.04009 ( 17) hydrogen bonds : angle 5.95897 ( 51) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 43 time to evaluate : 0.130 Fit side-chains REVERT: A 67 LYS cc_start: 0.8206 (tmtm) cc_final: 0.7986 (tmtp) REVERT: A 83 ASP cc_start: 0.6865 (t0) cc_final: 0.6624 (t0) REVERT: A 88 TYR cc_start: 0.7740 (m-80) cc_final: 0.7524 (m-80) REVERT: B 52 ASN cc_start: 0.7350 (t0) cc_final: 0.7116 (t0) REVERT: D 17 ARG cc_start: 0.6411 (ptm160) cc_final: 0.5550 (mmm160) REVERT: D 67 LYS cc_start: 0.8229 (tttm) cc_final: 0.7892 (tmtt) REVERT: D 83 ASP cc_start: 0.6924 (t0) cc_final: 0.6429 (t0) outliers start: 25 outliers final: 10 residues processed: 67 average time/residue: 0.3447 time to fit residues: 24.1847 Evaluate side-chains 47 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain F residue 40 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 ASN D 53 ASN E 28 ASN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN E 39 HIS F 28 ASN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 HIS F 80 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.176086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.166570 restraints weight = 5133.510| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 2.13 r_work: 0.4253 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4154 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 3678 Z= 0.408 Angle : 1.186 10.606 5010 Z= 0.642 Chirality : 0.063 0.268 540 Planarity : 0.009 0.076 660 Dihedral : 9.608 33.523 510 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 1.07 % Allowed : 29.06 % Favored : 69.87 % Rotamer: Outliers : 10.35 % Allowed : 35.10 % Favored : 54.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.33 % 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: -5.99 (0.23), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.56 (0.18), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 55 TYR 0.020 0.004 TYR E 88 PHE 0.034 0.007 PHE E 37 TRP 0.041 0.008 TRP D 92 HIS 0.008 0.002 HIS B 39 Details of bonding type rmsd covalent geometry : bond 0.00906 ( 3672) covalent geometry : angle 1.18675 ( 4998) SS BOND : bond 0.00840 ( 6) SS BOND : angle 1.06873 ( 12) hydrogen bonds : bond 0.04583 ( 17) hydrogen bonds : angle 7.16816 ( 51) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 40 time to evaluate : 0.137 Fit side-chains REVERT: A 67 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7842 (tmtp) REVERT: A 83 ASP cc_start: 0.7166 (t0) cc_final: 0.6856 (t0) REVERT: A 87 TYR cc_start: 0.7071 (OUTLIER) cc_final: 0.6238 (t80) REVERT: A 88 TYR cc_start: 0.8324 (m-80) cc_final: 0.8056 (m-80) REVERT: B 52 ASN cc_start: 0.7744 (t0) cc_final: 0.7488 (t0) REVERT: B 62 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6838 (tpm170) REVERT: B 87 TYR cc_start: 0.7068 (OUTLIER) cc_final: 0.5970 (t80) REVERT: C 28 ASN cc_start: 0.6816 (OUTLIER) cc_final: 0.6535 (m110) REVERT: C 83 ASP cc_start: 0.7005 (t0) cc_final: 0.6713 (t0) REVERT: D 17 ARG cc_start: 0.6712 (ptm160) cc_final: 0.5891 (mmm160) REVERT: D 67 LYS cc_start: 0.8209 (tttm) cc_final: 0.7917 (tmtt) REVERT: D 83 ASP cc_start: 0.7083 (t0) cc_final: 0.6778 (t0) REVERT: E 79 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8260 (mp) outliers start: 41 outliers final: 20 residues processed: 80 average time/residue: 0.3060 time to fit residues: 25.7258 Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 39 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 39 HIS Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain D residue 39 HIS Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 79 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 30 optimal weight: 0.4980 chunk 25 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN E 28 ASN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.185983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.176090 restraints weight = 5140.331| |-----------------------------------------------------------------------------| r_work (start): 0.4434 rms_B_bonded: 2.24 r_work: 0.4355 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4259 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3678 Z= 0.207 Angle : 0.932 7.568 5010 Z= 0.493 Chirality : 0.051 0.213 540 Planarity : 0.007 0.077 660 Dihedral : 8.579 27.472 510 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.85 % Allowed : 28.63 % Favored : 70.51 % Rotamer: Outliers : 7.32 % Allowed : 35.35 % Favored : 57.32 % 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: -5.75 (0.24), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.38 (0.18), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 62 TYR 0.013 0.003 TYR B 88 PHE 0.022 0.004 PHE E 37 TRP 0.022 0.004 TRP B 92 HIS 0.004 0.001 HIS F 39 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 3672) covalent geometry : angle 0.93262 ( 4998) SS BOND : bond 0.00296 ( 6) SS BOND : angle 0.76466 ( 12) hydrogen bonds : bond 0.03449 ( 17) hydrogen bonds : angle 6.63738 ( 51) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 37 time to evaluate : 0.088 Fit side-chains REVERT: A 59 VAL cc_start: 0.7374 (OUTLIER) cc_final: 0.7116 (m) REVERT: A 88 TYR cc_start: 0.8029 (m-80) cc_final: 0.7772 (m-80) REVERT: B 52 ASN cc_start: 0.7689 (t0) cc_final: 0.7459 (t0) REVERT: D 17 ARG cc_start: 0.6490 (ptm160) cc_final: 0.5640 (mmm160) REVERT: D 55 ARG cc_start: 0.7511 (ptp90) cc_final: 0.5659 (mmp-170) REVERT: D 67 LYS cc_start: 0.8259 (tttm) cc_final: 0.7795 (tmtt) REVERT: D 83 ASP cc_start: 0.7017 (t0) cc_final: 0.6526 (t0) REVERT: E 74 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8061 (tt) outliers start: 29 outliers final: 12 residues processed: 64 average time/residue: 0.3495 time to fit residues: 23.2571 Evaluate side-chains 47 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 79 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.200553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.190148 restraints weight = 4970.370| |-----------------------------------------------------------------------------| r_work (start): 0.4595 rms_B_bonded: 2.32 r_work: 0.4520 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4425 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3678 Z= 0.145 Angle : 0.804 7.147 5010 Z= 0.423 Chirality : 0.045 0.177 540 Planarity : 0.006 0.069 660 Dihedral : 7.286 23.715 510 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 28.21 % Favored : 71.79 % Rotamer: Outliers : 6.06 % Allowed : 34.85 % Favored : 59.09 % 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: -5.44 (0.26), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.14 (0.20), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 62 TYR 0.012 0.002 TYR B 50 PHE 0.011 0.002 PHE E 37 TRP 0.012 0.002 TRP C 36 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 3672) covalent geometry : angle 0.80428 ( 4998) SS BOND : bond 0.00092 ( 6) SS BOND : angle 0.42213 ( 12) hydrogen bonds : bond 0.02884 ( 17) hydrogen bonds : angle 6.26765 ( 51) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 47 time to evaluate : 0.096 Fit side-chains REVERT: A 17 ARG cc_start: 0.6575 (ptm160) cc_final: 0.6075 (tpp-160) REVERT: B 52 ASN cc_start: 0.7598 (t0) cc_final: 0.7340 (t0) REVERT: D 17 ARG cc_start: 0.6366 (ptm160) cc_final: 0.5564 (mmm160) REVERT: D 67 LYS cc_start: 0.8208 (tttm) cc_final: 0.7804 (tmtt) REVERT: D 83 ASP cc_start: 0.7049 (t0) cc_final: 0.6558 (t0) outliers start: 24 outliers final: 11 residues processed: 69 average time/residue: 0.2810 time to fit residues: 20.2321 Evaluate side-chains 53 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 79 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 53 ASN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 HIS ** 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 = 0.4579 r_free = 0.4579 target = 0.189931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.179514 restraints weight = 5102.820| |-----------------------------------------------------------------------------| r_work (start): 0.4479 rms_B_bonded: 2.28 r_work: 0.4398 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4301 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3678 Z= 0.213 Angle : 0.933 8.524 5010 Z= 0.491 Chirality : 0.049 0.211 540 Planarity : 0.008 0.102 660 Dihedral : 8.058 25.540 510 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 29.27 % Favored : 70.51 % Rotamer: Outliers : 7.07 % Allowed : 35.35 % Favored : 57.58 % 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: -5.50 (0.25), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.18 (0.19), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 62 TYR 0.014 0.003 TYR D 88 PHE 0.022 0.004 PHE E 37 TRP 0.022 0.004 TRP B 92 HIS 0.002 0.001 HIS B 39 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 3672) covalent geometry : angle 0.93380 ( 4998) SS BOND : bond 0.00345 ( 6) SS BOND : angle 0.69560 ( 12) hydrogen bonds : bond 0.02828 ( 17) hydrogen bonds : angle 6.44373 ( 51) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 42 time to evaluate : 0.132 Fit side-chains REVERT: A 17 ARG cc_start: 0.6693 (ptm160) cc_final: 0.6128 (tpp-160) REVERT: A 88 TYR cc_start: 0.8127 (m-80) cc_final: 0.7925 (m-80) REVERT: B 52 ASN cc_start: 0.7658 (t0) cc_final: 0.7453 (t0) REVERT: B 55 ARG cc_start: 0.7877 (pmm-80) cc_final: 0.7612 (pmm-80) REVERT: D 17 ARG cc_start: 0.6492 (ptm160) cc_final: 0.5588 (mmm160) REVERT: D 55 ARG cc_start: 0.7341 (ptp90) cc_final: 0.5873 (mmp-170) REVERT: D 67 LYS cc_start: 0.8166 (tttm) cc_final: 0.7729 (tmtt) REVERT: D 83 ASP cc_start: 0.7046 (t0) cc_final: 0.6542 (t0) outliers start: 28 outliers final: 17 residues processed: 66 average time/residue: 0.2756 time to fit residues: 18.9630 Evaluate side-chains 56 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 79 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 0.0970 chunk 37 optimal weight: 8.9990 chunk 44 optimal weight: 0.2980 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.200381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.189907 restraints weight = 5121.935| |-----------------------------------------------------------------------------| r_work (start): 0.4594 rms_B_bonded: 2.31 r_work: 0.4517 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4421 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3678 Z= 0.151 Angle : 0.842 7.338 5010 Z= 0.440 Chirality : 0.046 0.185 540 Planarity : 0.007 0.094 660 Dihedral : 7.396 23.803 510 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.92 % Favored : 73.08 % Rotamer: Outliers : 5.05 % Allowed : 37.12 % Favored : 57.83 % 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: -5.26 (0.26), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.20), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 62 TYR 0.012 0.002 TYR B 50 PHE 0.014 0.002 PHE E 37 TRP 0.012 0.002 TRP B 36 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 3672) covalent geometry : angle 0.84250 ( 4998) SS BOND : bond 0.00044 ( 6) SS BOND : angle 0.57075 ( 12) hydrogen bonds : bond 0.02669 ( 17) hydrogen bonds : angle 6.15912 ( 51) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.080 Fit side-chains REVERT: A 17 ARG cc_start: 0.6654 (ptm160) cc_final: 0.6063 (tpp-160) REVERT: D 17 ARG cc_start: 0.6509 (ptm160) cc_final: 0.5646 (mmm160) REVERT: D 67 LYS cc_start: 0.8166 (tttm) cc_final: 0.7767 (tmtt) REVERT: D 83 ASP cc_start: 0.7038 (t0) cc_final: 0.6613 (t0) outliers start: 20 outliers final: 12 residues processed: 60 average time/residue: 0.3935 time to fit residues: 24.4698 Evaluate side-chains 53 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 79 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 0.2980 chunk 30 optimal weight: 0.0030 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 53 ASN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.195341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.185020 restraints weight = 4990.604| |-----------------------------------------------------------------------------| r_work (start): 0.4542 rms_B_bonded: 2.24 r_work: 0.4465 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4371 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3678 Z= 0.184 Angle : 0.895 8.281 5010 Z= 0.470 Chirality : 0.047 0.191 540 Planarity : 0.007 0.091 660 Dihedral : 7.649 23.956 510 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.43 % Allowed : 28.21 % Favored : 71.37 % Rotamer: Outliers : 6.06 % Allowed : 36.36 % Favored : 57.58 % 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: -5.31 (0.26), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.20), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 62 TYR 0.013 0.002 TYR A 88 PHE 0.018 0.003 PHE E 37 TRP 0.017 0.003 TRP B 92 HIS 0.003 0.001 HIS F 39 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 3672) covalent geometry : angle 0.89570 ( 4998) SS BOND : bond 0.00208 ( 6) SS BOND : angle 0.63806 ( 12) hydrogen bonds : bond 0.02643 ( 17) hydrogen bonds : angle 6.16291 ( 51) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 43 time to evaluate : 0.134 Fit side-chains REVERT: A 17 ARG cc_start: 0.6697 (ptm160) cc_final: 0.6110 (tpp-160) REVERT: B 52 ASN cc_start: 0.7427 (t0) cc_final: 0.7164 (t0) REVERT: D 17 ARG cc_start: 0.6625 (ptm160) cc_final: 0.5665 (mmm160) REVERT: D 67 LYS cc_start: 0.8106 (tttm) cc_final: 0.7724 (tmtt) REVERT: D 83 ASP cc_start: 0.6947 (t0) cc_final: 0.6586 (t0) REVERT: E 79 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7825 (mp) outliers start: 24 outliers final: 15 residues processed: 64 average time/residue: 0.4206 time to fit residues: 28.0144 Evaluate side-chains 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.198753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.188100 restraints weight = 5141.617| |-----------------------------------------------------------------------------| r_work (start): 0.4568 rms_B_bonded: 2.31 r_work: 0.4490 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4393 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3678 Z= 0.165 Angle : 0.875 7.591 5010 Z= 0.458 Chirality : 0.047 0.189 540 Planarity : 0.007 0.089 660 Dihedral : 7.517 24.234 510 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 27.56 % Favored : 72.22 % Rotamer: Outliers : 4.55 % Allowed : 37.88 % Favored : 57.58 % 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: -5.25 (0.26), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.20), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 62 TYR 0.011 0.002 TYR B 50 PHE 0.017 0.003 PHE E 37 TRP 0.013 0.002 TRP A 92 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 3672) covalent geometry : angle 0.87528 ( 4998) SS BOND : bond 0.00124 ( 6) SS BOND : angle 0.57681 ( 12) hydrogen bonds : bond 0.02623 ( 17) hydrogen bonds : angle 6.08222 ( 51) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.129 Fit side-chains REVERT: A 17 ARG cc_start: 0.6668 (ptm160) cc_final: 0.6097 (tpp-160) REVERT: B 52 ASN cc_start: 0.7472 (t0) cc_final: 0.7090 (t0) REVERT: D 17 ARG cc_start: 0.6573 (ptm160) cc_final: 0.5661 (mmm160) REVERT: D 67 LYS cc_start: 0.8065 (tttm) cc_final: 0.7706 (tmtt) REVERT: D 83 ASP cc_start: 0.7048 (t0) cc_final: 0.6672 (t0) outliers start: 18 outliers final: 16 residues processed: 57 average time/residue: 0.4306 time to fit residues: 25.5059 Evaluate side-chains 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.0770 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.197526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.186963 restraints weight = 5036.753| |-----------------------------------------------------------------------------| r_work (start): 0.4575 rms_B_bonded: 2.30 r_work: 0.4494 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4396 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 3678 Z= 0.348 Angle : 1.813 59.185 5010 Z= 1.067 Chirality : 0.051 0.388 540 Planarity : 0.007 0.088 660 Dihedral : 7.869 38.094 510 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 27.56 % Favored : 72.22 % Rotamer: Outliers : 4.29 % Allowed : 38.13 % Favored : 57.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -5.25 (0.26), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.20), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.011 0.002 TYR B 50 PHE 0.017 0.003 PHE E 37 TRP 0.013 0.002 TRP E 92 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00617 ( 3672) covalent geometry : angle 1.81536 ( 4998) SS BOND : bond 0.00089 ( 6) SS BOND : angle 0.56660 ( 12) hydrogen bonds : bond 0.02607 ( 17) hydrogen bonds : angle 6.07725 ( 51) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1265.45 seconds wall clock time: 22 minutes 24.32 seconds (1344.32 seconds total)