Starting phenix.real_space_refine on Tue Aug 4 12:06:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9far_50279/08_2026/9far_50279.cif Found real_map, /net/cci-nas-00/data/ceres_data/9far_50279/08_2026/9far_50279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9far_50279/08_2026/9far_50279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9far_50279/08_2026/9far_50279.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9far_50279/08_2026/9far_50279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9far_50279/08_2026/9far_50279.map" } resolution = 2.9 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 23 5.16 5 Cl 1 4.86 5 C 1591 2.51 5 N 341 2.21 5 O 388 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2345 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 471 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'P1L:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 255 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "L" Number of atoms: 1515 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 193, 1500 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Conformer: "B" Number of residues, atoms: 193, 1500 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} bond proxies already assigned to first conformer: 1523 Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {'CLR': 1, 'D10': 1, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {' CL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.14, per 1000 atoms: 0.49 Number of scatterers: 2345 At special positions: 0 Unit cell: (53.129, 56.3009, 84.0548, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 23 16.00 P 1 15.00 O 388 8.00 N 341 7.00 C 1591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 77 " distance=2.03 Simple disulfide: pdb=" SG CYS L 109 " - pdb=" SG CYS L 128 " distance=2.04 Simple disulfide: pdb=" SG CYS L 159 " - pdb=" SG CYS L 171 " 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: 0.23 Conformation dependent library (CDL) restraints added in 77.3 milliseconds 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 520 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 1 sheets defined 71.5% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing helix chain 'C' and resid 374 through 379 Processing helix chain 'C' and resid 401 through 427 removed outlier: 4.243A pdb=" N ILE C 408 " --> pdb=" O SER C 404 " (cutoff:3.500A) Proline residue: C 411 - end of helix Processing helix chain 'H' and resid 672 through 699 Processing helix chain 'L' and resid 12 through 43 Processing helix chain 'L' and resid 83 through 87 removed outlier: 3.649A pdb=" N THR L 86 " --> pdb=" O ASP L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 113 Processing helix chain 'L' and resid 114 through 117 removed outlier: 3.623A pdb=" N PHE L 117 " --> pdb=" O SER L 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 114 through 117' Processing helix chain 'L' and resid 120 through 146 Processing helix chain 'L' and resid 147 through 151 removed outlier: 4.056A pdb=" N ASP L 151 " --> pdb=" O ASP L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 160 Processing helix chain 'L' and resid 174 through 203 removed outlier: 3.786A pdb=" N ILE L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR L 202 " --> pdb=" O GLY L 198 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP L 203 " --> pdb=" O ASN L 199 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 76 through 78 157 hydrogen bonds defined for protein. 452 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: 0.20 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 330 1.31 - 1.44: 710 1.44 - 1.56: 1333 1.56 - 1.69: 2 1.69 - 1.82: 32 Bond restraints: 2407 Sorted by residual: bond pdb=" C1 PGW L 301 " pdb=" O01 PGW L 301 " ideal model delta sigma weight residual 1.332 1.415 -0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C19 PGW L 301 " pdb=" O03 PGW L 301 " ideal model delta sigma weight residual 1.332 1.412 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" N ASP H 671 " pdb=" CA ASP H 671 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 6.85e+00 bond pdb=" N VAL H 680 " pdb=" CA VAL H 680 " ideal model delta sigma weight residual 1.460 1.491 -0.031 1.21e-02 6.83e+03 6.54e+00 bond pdb=" N GLU C 383 " pdb=" CA GLU C 383 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.31e-02 5.83e+03 6.50e+00 ... (remaining 2402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.80: 3189 3.80 - 7.60: 44 7.60 - 11.40: 5 11.40 - 15.21: 0 15.21 - 19.01: 1 Bond angle restraints: 3239 Sorted by residual: angle pdb=" CB P1L C 380 " pdb=" SG P1L C 380 " pdb=" C7 P1L C 380 " ideal model delta sigma weight residual 102.31 121.32 -19.01 3.00e+00 1.11e-01 4.01e+01 angle pdb=" CA ASP C 374 " pdb=" C ASP C 374 " pdb=" O ASP C 374 " ideal model delta sigma weight residual 122.03 117.71 4.32 1.13e+00 7.83e-01 1.46e+01 angle pdb=" O13 PGW L 301 " pdb=" P PGW L 301 " pdb=" O14 PGW L 301 " ideal model delta sigma weight residual 119.81 109.21 10.60 3.00e+00 1.11e-01 1.25e+01 angle pdb=" N GLU C 383 " pdb=" CA GLU C 383 " pdb=" C GLU C 383 " ideal model delta sigma weight residual 114.31 109.88 4.43 1.29e+00 6.01e-01 1.18e+01 angle pdb=" N GLY C 372 " pdb=" CA GLY C 372 " pdb=" C GLY C 372 " ideal model delta sigma weight residual 114.90 109.70 5.20 1.54e+00 4.22e-01 1.14e+01 ... (remaining 3234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 1423 35.60 - 71.20: 46 71.20 - 106.80: 4 106.80 - 142.40: 2 142.40 - 178.00: 1 Dihedral angle restraints: 1476 sinusoidal: 664 harmonic: 812 Sorted by residual: dihedral pdb=" C07 PGW L 301 " pdb=" C06 PGW L 301 " pdb=" C10 PGW L 301 " pdb=" C9 PGW L 301 " ideal model delta sinusoidal sigma weight residual 110.06 -71.94 -178.00 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O12 PGW L 301 " pdb=" C04 PGW L 301 " pdb=" C05 PGW L 301 " pdb=" OAF PGW L 301 " ideal model delta sinusoidal sigma weight residual 69.27 -157.62 -133.11 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" CAD PGW L 301 " pdb=" C04 PGW L 301 " pdb=" C05 PGW L 301 " pdb=" O12 PGW L 301 " ideal model delta sinusoidal sigma weight residual 168.74 37.55 131.19 1 3.00e+01 1.11e-03 1.77e+01 ... (remaining 1473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 299 0.061 - 0.122: 46 0.122 - 0.184: 7 0.184 - 0.245: 0 0.245 - 0.306: 3 Chirality restraints: 355 Sorted by residual: chirality pdb=" CA P1L C 385 " pdb=" N P1L C 385 " pdb=" C P1L C 385 " pdb=" CB P1L C 385 " both_signs ideal model delta sigma weight residual False 2.32 2.62 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA P1L C 380 " pdb=" N P1L C 380 " pdb=" C P1L C 380 " pdb=" CB P1L C 380 " both_signs ideal model delta sigma weight residual False 2.32 2.62 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA P1L C 381 " pdb=" N P1L C 381 " pdb=" C P1L C 381 " pdb=" CB P1L C 381 " both_signs ideal model delta sigma weight residual False 2.32 2.59 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 352 not shown) Planarity restraints: 379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA P1L C 380 " 0.017 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C P1L C 380 " -0.063 2.00e-02 2.50e+03 pdb=" O P1L C 380 " 0.023 2.00e-02 2.50e+03 pdb=" N P1L C 381 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG L 73 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C ARG L 73 " 0.027 2.00e-02 2.50e+03 pdb=" O ARG L 73 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU L 74 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 668 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C ASP H 668 " -0.025 2.00e-02 2.50e+03 pdb=" O ASP H 668 " 0.009 2.00e-02 2.50e+03 pdb=" N SER H 669 " 0.008 2.00e-02 2.50e+03 ... (remaining 376 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 106 2.73 - 3.27: 2471 3.27 - 3.81: 3762 3.81 - 4.36: 4614 4.36 - 4.90: 7978 Nonbonded interactions: 18931 Sorted by model distance: nonbonded pdb=" O12 PGW L 301 " pdb=" OAE PGW L 301 " model vdw 2.187 3.040 nonbonded pdb=" O PHE L 117 " pdb=" OAE PGW L 301 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR H 672 " pdb=" OD1 ASP L 49 " model vdw 2.400 3.040 nonbonded pdb=" O1 CLR C 502 " pdb="CL CL L 302 " model vdw 2.430 3.190 nonbonded pdb=" O GLY L 79 " pdb=" OG SER L 80 " model vdw 2.458 3.040 ... (remaining 18926 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=0.99 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: 1.240 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.200 Find NCS groups from input model: 0.010 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:5.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 0.007 0.083 2410 Z= 0.383 Angle : 1.085 19.008 3245 Z= 0.536 Chirality : 0.053 0.306 355 Planarity : 0.004 0.036 379 Dihedral : 17.920 177.997 947 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.87 % Allowed : 2.17 % Favored : 96.96 % 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: 1.29 (0.53), residues: 266 helix: 1.91 (0.37), residues: 176 sheet: -2.11 (1.41), residues: 13 loop : -1.09 (0.81), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 670 TYR 0.013 0.001 TYR L 15 PHE 0.012 0.001 PHE L 59 TRP 0.006 0.001 TRP L 130 HIS 0.002 0.001 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.38 ( 2407) covalent geometry : angle 1.08159 / 0.53 ( 3239) SS BOND : bond 0.00360 / 0.17 ( 3) SS BOND : angle 2.25767 / 0.90 ( 6) hydrogen bonds : bond 0.12515 / 7.47 ( 157) hydrogen bonds : angle 5.56474 / 3.65 ( 452) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.058 Fit side-chains revert: symmetry clash REVERT: H 673 SER cc_start: 0.8785 (t) cc_final: 0.8289 (m) REVERT: H 677 SER cc_start: 0.8811 (t) cc_final: 0.8589 (p) outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.2108 time to fit residues: 10.3831 Evaluate side-chains 33 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 384 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 ASN ** 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 = 0.3829 r_free = 0.3829 target = 0.132081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.093472 restraints weight = 17537.068| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 6.62 r_work: 0.2975 rms_B_bonded: 6.54 restraints_weight: 2.0000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2410 Z= 0.163 Angle : 0.631 9.624 3245 Z= 0.317 Chirality : 0.042 0.154 355 Planarity : 0.003 0.023 379 Dihedral : 16.399 155.161 499 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.61 % Allowed : 11.30 % Favored : 86.09 % 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: 1.81 (0.52), residues: 266 helix: 2.55 (0.36), residues: 172 sheet: -1.83 (1.44), residues: 13 loop : -1.35 (0.71), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 670 TYR 0.021 0.002 TYR L 64 PHE 0.017 0.002 PHE L 117 TRP 0.009 0.001 TRP L 130 HIS 0.002 0.001 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 2407) covalent geometry : angle 0.62874 / 0.32 ( 3239) SS BOND : bond 0.00468 / 0.23 ( 3) SS BOND : angle 1.37489 / 0.60 ( 6) hydrogen bonds : bond 0.04154 / 2.29 ( 157) hydrogen bonds : angle 4.17986 / 2.85 ( 452) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: C 404 SER cc_start: 0.9021 (t) cc_final: 0.8750 (p) REVERT: H 673 SER cc_start: 0.8594 (t) cc_final: 0.8325 (m) REVERT: L 55 LYS cc_start: 0.8347 (ttpt) cc_final: 0.8104 (ttpp) REVERT: L 74 GLU cc_start: 0.6889 (mp0) cc_final: 0.6624 (mp0) outliers start: 6 outliers final: 1 residues processed: 43 average time/residue: 0.3546 time to fit residues: 15.7773 Evaluate side-chains 37 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 690 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.130492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.091340 restraints weight = 16321.050| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 5.30 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2410 Z= 0.146 Angle : 0.593 9.382 3245 Z= 0.296 Chirality : 0.040 0.148 355 Planarity : 0.003 0.021 379 Dihedral : 15.031 131.095 497 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.17 % Allowed : 12.61 % Favored : 85.22 % 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: 2.12 (0.52), residues: 266 helix: 2.81 (0.36), residues: 172 sheet: -1.71 (1.45), residues: 13 loop : -1.29 (0.71), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 670 TYR 0.016 0.001 TYR L 15 PHE 0.011 0.001 PHE L 59 TRP 0.007 0.001 TRP L 130 HIS 0.002 0.001 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 2407) covalent geometry : angle 0.59168 / 0.30 ( 3239) SS BOND : bond 0.00450 / 0.22 ( 3) SS BOND : angle 0.93675 / 0.43 ( 6) hydrogen bonds : bond 0.03925 / 2.21 ( 157) hydrogen bonds : angle 4.01893 / 2.75 ( 452) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: H 673 SER cc_start: 0.8684 (t) cc_final: 0.8363 (m) REVERT: L 74 GLU cc_start: 0.6756 (mp0) cc_final: 0.6482 (mp0) REVERT: L 148 ASP cc_start: 0.8462 (t0) cc_final: 0.8219 (t0) outliers start: 5 outliers final: 2 residues processed: 42 average time/residue: 0.3799 time to fit residues: 16.4945 Evaluate side-chains 35 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 399 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 690 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.129727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.091132 restraints weight = 14859.637| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 5.13 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2410 Z= 0.144 Angle : 0.593 9.981 3245 Z= 0.296 Chirality : 0.041 0.165 355 Planarity : 0.003 0.020 379 Dihedral : 14.063 96.306 497 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.74 % Allowed : 15.22 % Favored : 83.04 % 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: 2.11 (0.52), residues: 266 helix: 2.84 (0.37), residues: 172 sheet: -1.87 (1.39), residues: 13 loop : -1.37 (0.70), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 78 TYR 0.016 0.001 TYR L 15 PHE 0.012 0.001 PHE L 117 TRP 0.010 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 2407) covalent geometry : angle 0.58482 / 0.29 ( 3239) SS BOND : bond 0.00700 / 0.33 ( 3) SS BOND : angle 2.35883 / 0.93 ( 6) hydrogen bonds : bond 0.04016 / 2.25 ( 157) hydrogen bonds : angle 4.03579 / 2.77 ( 452) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: H 673 SER cc_start: 0.8661 (t) cc_final: 0.8314 (m) REVERT: L 74 GLU cc_start: 0.6699 (mp0) cc_final: 0.6453 (mp0) outliers start: 4 outliers final: 1 residues processed: 40 average time/residue: 0.2862 time to fit residues: 11.9494 Evaluate side-chains 35 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 2 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.129510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.090526 restraints weight = 13315.849| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 4.93 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2410 Z= 0.137 Angle : 0.597 10.573 3245 Z= 0.294 Chirality : 0.040 0.135 355 Planarity : 0.003 0.018 379 Dihedral : 12.842 58.151 497 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.48 % Allowed : 16.52 % Favored : 80.00 % 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: 2.21 (0.52), residues: 266 helix: 2.86 (0.37), residues: 176 sheet: -1.69 (1.42), residues: 13 loop : -1.43 (0.71), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 670 TYR 0.014 0.001 TYR L 15 PHE 0.011 0.001 PHE L 59 TRP 0.007 0.001 TRP L 130 HIS 0.002 0.001 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 2407) covalent geometry : angle 0.59273 / 0.29 ( 3239) SS BOND : bond 0.00428 / 0.21 ( 3) SS BOND : angle 1.72173 / 0.68 ( 6) hydrogen bonds : bond 0.03901 / 2.18 ( 157) hydrogen bonds : angle 3.95600 / 2.70 ( 452) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.087 Fit side-chains REVERT: C 407 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.4265 (mmt90) REVERT: H 673 SER cc_start: 0.8672 (t) cc_final: 0.8316 (m) REVERT: L 16 MET cc_start: 0.6298 (tmm) cc_final: 0.6034 (tmt) REVERT: L 74 GLU cc_start: 0.6614 (mp0) cc_final: 0.6391 (mp0) outliers start: 8 outliers final: 3 residues processed: 42 average time/residue: 0.3244 time to fit residues: 14.1617 Evaluate side-chains 38 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 407 ARG Chi-restraints excluded: chain H residue 686 LEU Chi-restraints excluded: chain L residue 154 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.127865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.089011 restraints weight = 17573.814| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 5.46 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2410 Z= 0.150 Angle : 0.616 9.134 3245 Z= 0.302 Chirality : 0.041 0.137 355 Planarity : 0.003 0.018 379 Dihedral : 12.561 59.821 497 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.17 % Allowed : 18.26 % Favored : 79.57 % 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: 2.15 (0.52), residues: 266 helix: 2.78 (0.36), residues: 177 sheet: -1.68 (1.42), residues: 13 loop : -1.44 (0.72), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 670 TYR 0.014 0.001 TYR L 15 PHE 0.012 0.001 PHE L 117 TRP 0.008 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 2407) covalent geometry : angle 0.61483 / 0.30 ( 3239) SS BOND : bond 0.00585 / 0.28 ( 3) SS BOND : angle 1.20783 / 0.49 ( 6) hydrogen bonds : bond 0.03961 / 2.21 ( 157) hydrogen bonds : angle 3.99091 / 2.72 ( 452) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.092 Fit side-chains REVERT: C 407 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.4281 (mmt90) REVERT: H 673 SER cc_start: 0.8679 (t) cc_final: 0.8315 (m) REVERT: L 16 MET cc_start: 0.6370 (tmm) cc_final: 0.6094 (tmt) REVERT: L 74 GLU cc_start: 0.6721 (mp0) cc_final: 0.6467 (mp0) outliers start: 5 outliers final: 1 residues processed: 37 average time/residue: 0.3553 time to fit residues: 13.6280 Evaluate side-chains 35 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 407 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.126705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.088269 restraints weight = 20698.555| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 5.52 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2410 Z= 0.158 Angle : 0.633 8.322 3245 Z= 0.308 Chirality : 0.040 0.137 355 Planarity : 0.003 0.017 379 Dihedral : 12.411 60.363 497 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.35 % Allowed : 16.52 % Favored : 79.13 % 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: 2.10 (0.52), residues: 266 helix: 2.82 (0.36), residues: 176 sheet: -1.78 (1.36), residues: 13 loop : -1.61 (0.70), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 670 TYR 0.014 0.001 TYR L 15 PHE 0.012 0.001 PHE L 59 TRP 0.008 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 2407) covalent geometry : angle 0.63141 / 0.31 ( 3239) SS BOND : bond 0.00478 / 0.23 ( 3) SS BOND : angle 1.08622 / 0.45 ( 6) hydrogen bonds : bond 0.03975 / 2.22 ( 157) hydrogen bonds : angle 4.00448 / 2.73 ( 452) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.051 Fit side-chains REVERT: C 407 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.4237 (mmt90) REVERT: H 673 SER cc_start: 0.8669 (t) cc_final: 0.8288 (m) REVERT: L 16 MET cc_start: 0.6391 (tmm) cc_final: 0.6140 (tmt) REVERT: L 74 GLU cc_start: 0.6749 (mp0) cc_final: 0.6367 (mp0) outliers start: 10 outliers final: 6 residues processed: 42 average time/residue: 0.3571 time to fit residues: 15.5001 Evaluate side-chains 42 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 407 ARG Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain H residue 685 SER Chi-restraints excluded: chain H residue 686 LEU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 154 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 0.0040 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.129442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.097771 restraints weight = 16356.909| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 7.10 r_work: 0.2959 rms_B_bonded: 6.38 restraints_weight: 2.0000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2410 Z= 0.115 Angle : 0.615 10.665 3245 Z= 0.291 Chirality : 0.040 0.222 355 Planarity : 0.003 0.018 379 Dihedral : 11.839 59.800 497 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.61 % Allowed : 19.13 % Favored : 78.26 % 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: 2.17 (0.53), residues: 266 helix: 2.90 (0.36), residues: 176 sheet: -1.76 (1.37), residues: 13 loop : -1.65 (0.72), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 670 TYR 0.012 0.001 TYR L 15 PHE 0.010 0.001 PHE L 117 TRP 0.004 0.001 TRP C 422 HIS 0.002 0.001 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 2407) covalent geometry : angle 0.61432 / 0.29 ( 3239) SS BOND : bond 0.00346 / 0.17 ( 3) SS BOND : angle 0.78354 / 0.34 ( 6) hydrogen bonds : bond 0.03816 / 2.14 ( 157) hydrogen bonds : angle 3.99536 / 2.70 ( 452) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.081 Fit side-chains REVERT: C 407 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.4358 (mmt90) REVERT: H 673 SER cc_start: 0.8641 (t) cc_final: 0.8343 (m) REVERT: L 16 MET cc_start: 0.6341 (tmm) cc_final: 0.6127 (tmt) REVERT: L 74 GLU cc_start: 0.6617 (mp0) cc_final: 0.6373 (mp0) outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 0.2910 time to fit residues: 11.8013 Evaluate side-chains 39 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 407 ARG Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain H residue 689 LEU Chi-restraints excluded: chain L residue 154 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.128230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.096021 restraints weight = 15629.360| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 7.12 r_work: 0.2929 rms_B_bonded: 6.32 restraints_weight: 2.0000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2410 Z= 0.139 Angle : 0.635 10.677 3245 Z= 0.304 Chirality : 0.042 0.244 355 Planarity : 0.003 0.016 379 Dihedral : 11.974 62.763 497 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.17 % Allowed : 18.70 % Favored : 79.13 % 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: 2.07 (0.52), residues: 266 helix: 2.90 (0.37), residues: 172 sheet: -1.75 (1.34), residues: 13 loop : -1.65 (0.69), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 200 TYR 0.014 0.001 TYR L 15 PHE 0.012 0.001 PHE L 117 TRP 0.008 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 2407) covalent geometry : angle 0.63503 / 0.30 ( 3239) SS BOND : bond 0.00476 / 0.23 ( 3) SS BOND : angle 0.82388 / 0.35 ( 6) hydrogen bonds : bond 0.03860 / 2.16 ( 157) hydrogen bonds : angle 4.06124 / 2.75 ( 452) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.054 Fit side-chains REVERT: C 407 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.4325 (mmt90) REVERT: H 673 SER cc_start: 0.8631 (t) cc_final: 0.8321 (m) REVERT: H 690 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8740 (m110) REVERT: L 16 MET cc_start: 0.6323 (tmm) cc_final: 0.6116 (tmt) REVERT: L 74 GLU cc_start: 0.6672 (mp0) cc_final: 0.6387 (mp0) outliers start: 5 outliers final: 4 residues processed: 36 average time/residue: 0.2729 time to fit residues: 10.1305 Evaluate side-chains 39 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 407 ARG Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain H residue 689 LEU Chi-restraints excluded: chain H residue 690 ASN Chi-restraints excluded: chain L residue 154 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.127145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.094245 restraints weight = 15794.060| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 7.03 r_work: 0.2917 rms_B_bonded: 6.24 restraints_weight: 2.0000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2410 Z= 0.157 Angle : 0.648 10.340 3245 Z= 0.310 Chirality : 0.042 0.234 355 Planarity : 0.003 0.016 379 Dihedral : 12.125 65.012 497 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.61 % Allowed : 18.26 % Favored : 79.13 % 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: 2.01 (0.52), residues: 266 helix: 2.76 (0.36), residues: 176 sheet: -1.79 (1.33), residues: 13 loop : -1.68 (0.71), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 670 TYR 0.014 0.001 TYR L 15 PHE 0.013 0.001 PHE L 59 TRP 0.008 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 2407) covalent geometry : angle 0.64755 / 0.31 ( 3239) SS BOND : bond 0.00499 / 0.24 ( 3) SS BOND : angle 0.85322 / 0.37 ( 6) hydrogen bonds : bond 0.03915 / 2.19 ( 157) hydrogen bonds : angle 4.07661 / 2.75 ( 452) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.052 Fit side-chains REVERT: C 407 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.4311 (mmt90) REVERT: H 673 SER cc_start: 0.8644 (t) cc_final: 0.8327 (m) REVERT: H 690 ASN cc_start: 0.9119 (OUTLIER) cc_final: 0.8765 (m110) REVERT: L 16 MET cc_start: 0.6333 (tmm) cc_final: 0.6130 (tmt) REVERT: L 74 GLU cc_start: 0.6774 (mp0) cc_final: 0.6498 (mp0) outliers start: 6 outliers final: 3 residues processed: 35 average time/residue: 0.2554 time to fit residues: 9.2332 Evaluate side-chains 37 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 407 ARG Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain H residue 690 ASN Chi-restraints excluded: chain L residue 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 18 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.128080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.089511 restraints weight = 11292.302| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 4.48 r_work: 0.3003 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2410 Z= 0.137 Angle : 0.643 12.138 3245 Z= 0.305 Chirality : 0.042 0.291 355 Planarity : 0.003 0.016 379 Dihedral : 12.035 65.387 497 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.61 % Allowed : 18.70 % Favored : 78.70 % 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: 2.07 (0.52), residues: 266 helix: 2.80 (0.37), residues: 176 sheet: -1.76 (1.34), residues: 13 loop : -1.64 (0.71), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 670 TYR 0.014 0.001 TYR L 15 PHE 0.011 0.001 PHE L 59 TRP 0.007 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 2407) covalent geometry : angle 0.64281 / 0.31 ( 3239) SS BOND : bond 0.00448 / 0.21 ( 3) SS BOND : angle 0.77407 / 0.33 ( 6) hydrogen bonds : bond 0.03893 / 2.17 ( 157) hydrogen bonds : angle 4.07721 / 2.76 ( 452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 946.06 seconds wall clock time: 16 minutes 49.85 seconds (1009.85 seconds total)