Starting phenix.real_space_refine on Wed Jul 1 21:04:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9far_50279/07_2026/9far_50279.cif Found real_map, /net/cci-nas-00/data/ceres_data/9far_50279/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9far_50279/07_2026/9far_50279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9far_50279/07_2026/9far_50279.map" model { file = "/net/cci-nas-00/data/ceres_data/9far_50279/07_2026/9far_50279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9far_50279/07_2026/9far_50279.cif" } 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-dev-6108/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, 51 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 1.00, per 1000 atoms: 0.43 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 82.5 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: 0.03 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: 0.21 Time building geometry restraints manager: 0.22 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 3.270 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.340 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:5.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.690 ------------------------------------------------------------------------------- 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 : 0.051 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: 0.1636 time to fit residues: 8.0543 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: 0.5980 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: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.132444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.093775 restraints weight = 17533.238| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 6.61 r_work: 0.2978 rms_B_bonded: 6.53 restraints_weight: 2.0000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 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 = 0.2968 r_free = 0.2968 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 (10 function evaluations) r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2410 Z= 0.158 Angle : 0.627 9.341 3245 Z= 0.315 Chirality : 0.042 0.162 355 Planarity : 0.003 0.022 379 Dihedral : 16.293 153.056 499 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.17 % Allowed : 11.30 % Favored : 86.52 % 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: 1.85 (0.52), residues: 266 helix: 2.57 (0.37), residues: 172 sheet: -1.85 (1.44), residues: 13 loop : -1.31 (0.72), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 670 TYR 0.020 0.002 TYR L 64 PHE 0.016 0.002 PHE L 117 TRP 0.008 0.001 TRP L 130 HIS 0.002 0.001 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 2407) covalent geometry : angle 0.62463 / 0.31 ( 3239) SS BOND : bond 0.00463 / 0.22 ( 3) SS BOND : angle 1.29329 / 0.57 ( 6) hydrogen bonds : bond 0.04169 / 2.31 ( 157) hydrogen bonds : angle 4.17303 / 2.84 ( 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 43 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.052 Fit side-chains revert: symmetry clash REVERT: C 404 SER cc_start: 0.9010 (t) cc_final: 0.8748 (p) REVERT: H 673 SER cc_start: 0.8614 (t) cc_final: 0.8340 (m) REVERT: H 699 TYR cc_start: 0.6060 (t80) cc_final: 0.5851 (t80) REVERT: L 55 LYS cc_start: 0.8355 (ttpt) cc_final: 0.8115 (ttpp) REVERT: L 74 GLU cc_start: 0.6873 (mp0) cc_final: 0.6614 (mp0) outliers start: 5 outliers final: 0 residues processed: 43 average time/residue: 0.2322 time to fit residues: 10.3501 Evaluate side-chains 36 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.130562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.091321 restraints weight = 16333.734| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 5.31 r_work (final): 0.3238 ------------------------------------------------------------------------------- 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: 0.8523 moved from start: 0.2456 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= 0.145 Angle : 0.596 9.486 3245 Z= 0.297 Chirality : 0.041 0.151 355 Planarity : 0.003 0.020 379 Dihedral : 14.894 127.761 497 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.17 % Allowed : 13.48 % Favored : 84.35 % 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: 2.80 (0.37), residues: 172 sheet: -1.74 (1.44), residues: 13 loop : -1.33 (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 0.001 0.001 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 ( 2407) covalent geometry : angle 0.59470 / 0.30 ( 3239) SS BOND : bond 0.00468 / 0.22 ( 3) SS BOND : angle 0.94163 / 0.44 ( 6) hydrogen bonds : bond 0.03929 / 2.20 ( 157) hydrogen bonds : angle 4.01949 / 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 45 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.053 Fit side-chains revert: symmetry clash REVERT: H 673 SER cc_start: 0.8698 (t) cc_final: 0.8369 (m) REVERT: L 74 GLU cc_start: 0.6775 (mp0) cc_final: 0.6501 (mp0) REVERT: L 148 ASP cc_start: 0.8465 (t0) cc_final: 0.8229 (t0) outliers start: 5 outliers final: 2 residues processed: 43 average time/residue: 0.2405 time to fit residues: 10.6878 Evaluate side-chains 36 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.057 ------------------------------------------------------------------------------- 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: 0.8980 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 0.0770 chunk 14 optimal weight: 0.0870 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 690 ASN L 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.131456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.098208 restraints weight = 14834.862| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 6.95 r_work: 0.2973 rms_B_bonded: 6.51 restraints_weight: 2.0000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2410 Z= 0.122 Angle : 0.576 10.126 3245 Z= 0.287 Chirality : 0.039 0.156 355 Planarity : 0.003 0.019 379 Dihedral : 13.762 93.312 497 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.30 % Allowed : 15.22 % Favored : 83.48 % 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: 2.19 (0.52), residues: 266 helix: 2.93 (0.37), residues: 172 sheet: -1.96 (1.39), residues: 13 loop : -1.39 (0.69), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 670 TYR 0.015 0.001 TYR L 15 PHE 0.012 0.001 PHE L 117 TRP 0.009 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 2407) covalent geometry : angle 0.56780 / 0.28 ( 3239) SS BOND : bond 0.00805 / 0.38 ( 3) SS BOND : angle 2.31293 / 0.91 ( 6) hydrogen bonds : bond 0.03898 / 2.18 ( 157) hydrogen bonds : angle 3.98416 / 2.74 ( 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 40 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: H 673 SER cc_start: 0.8600 (t) cc_final: 0.8333 (m) REVERT: L 16 MET cc_start: 0.6205 (tmm) cc_final: 0.5962 (tmt) outliers start: 3 outliers final: 0 residues processed: 40 average time/residue: 0.2431 time to fit residues: 10.1901 Evaluate side-chains 33 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 25 optimal weight: 0.0870 chunk 2 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.130316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.089855 restraints weight = 13125.333| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 4.34 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2922 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= 0.126 Angle : 0.582 8.517 3245 Z= 0.290 Chirality : 0.039 0.136 355 Planarity : 0.003 0.019 379 Dihedral : 12.809 59.275 497 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.74 % Allowed : 16.09 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.28 (0.52), residues: 266 helix: 3.02 (0.37), residues: 172 sheet: -1.80 (1.42), residues: 13 loop : -1.42 (0.68), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 73 TYR 0.024 0.002 TYR L 64 PHE 0.010 0.001 PHE L 59 TRP 0.006 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 2407) covalent geometry : angle 0.57873 / 0.29 ( 3239) SS BOND : bond 0.00544 / 0.26 ( 3) SS BOND : angle 1.55040 / 0.61 ( 6) hydrogen bonds : bond 0.03841 / 2.14 ( 157) hydrogen bonds : angle 3.92035 / 2.67 ( 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 41 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.088 Fit side-chains REVERT: H 673 SER cc_start: 0.8626 (t) cc_final: 0.8275 (m) REVERT: L 16 MET cc_start: 0.6341 (tmm) cc_final: 0.6103 (tmt) outliers start: 4 outliers final: 2 residues processed: 40 average time/residue: 0.2753 time to fit residues: 11.5211 Evaluate side-chains 36 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain H residue 686 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.0870 chunk 18 optimal weight: 0.1980 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.130379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.091712 restraints weight = 17459.745| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 5.42 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 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 = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3209 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= 0.124 Angle : 0.590 7.646 3245 Z= 0.292 Chirality : 0.039 0.141 355 Planarity : 0.003 0.018 379 Dihedral : 12.336 58.644 497 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.61 % Allowed : 16.52 % Favored : 80.87 % 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: 2.28 (0.52), residues: 266 helix: 2.91 (0.37), residues: 177 sheet: -1.84 (1.37), residues: 13 loop : -1.43 (0.71), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 670 TYR 0.013 0.001 TYR L 64 PHE 0.012 0.001 PHE L 117 TRP 0.006 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 2407) covalent geometry : angle 0.58817 / 0.29 ( 3239) SS BOND : bond 0.00423 / 0.20 ( 3) SS BOND : angle 1.19248 / 0.48 ( 6) hydrogen bonds : bond 0.03785 / 2.12 ( 157) hydrogen bonds : angle 3.89087 / 2.64 ( 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 40 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.095 Fit side-chains REVERT: C 407 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.4278 (mmt90) REVERT: H 673 SER cc_start: 0.8653 (t) cc_final: 0.8305 (m) REVERT: L 16 MET cc_start: 0.6406 (tmm) cc_final: 0.6200 (tmt) outliers start: 6 outliers final: 3 residues processed: 39 average time/residue: 0.3686 time to fit residues: 14.8950 Evaluate side-chains 37 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.085 ------------------------------------------------------------------------------- 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 416 LEU Chi-restraints excluded: chain L residue 154 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.127282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.087537 restraints weight = 20882.504| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 5.81 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3329 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= 0.180 Angle : 0.645 7.687 3245 Z= 0.319 Chirality : 0.041 0.136 355 Planarity : 0.003 0.021 379 Dihedral : 12.558 57.945 497 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.61 % Allowed : 17.83 % 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: 2.07 (0.52), residues: 266 helix: 2.74 (0.37), residues: 177 sheet: -1.64 (1.45), residues: 13 loop : -1.56 (0.69), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 407 TYR 0.014 0.001 TYR L 15 PHE 0.014 0.001 PHE L 117 TRP 0.011 0.001 TRP L 130 HIS 0.002 0.001 HIS L 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 ( 2407) covalent geometry : angle 0.64315 / 0.32 ( 3239) SS BOND : bond 0.00579 / 0.28 ( 3) SS BOND : angle 1.21180 / 0.50 ( 6) hydrogen bonds : bond 0.04020 / 2.24 ( 157) hydrogen bonds : angle 4.09546 / 2.79 ( 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 39 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.087 Fit side-chains REVERT: C 407 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.4241 (mmt90) REVERT: H 673 SER cc_start: 0.8683 (t) cc_final: 0.8318 (m) outliers start: 6 outliers final: 4 residues processed: 38 average time/residue: 0.3518 time to fit residues: 13.8154 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 : 0.050 ------------------------------------------------------------------------------- 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 C residue 416 LEU 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: 0.9990 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 8.9990 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.127090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.094801 restraints weight = 16397.787| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 6.88 r_work: 0.2907 rms_B_bonded: 6.37 restraints_weight: 2.0000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 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: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2410 Z= 0.154 Angle : 0.629 8.058 3245 Z= 0.311 Chirality : 0.040 0.137 355 Planarity : 0.003 0.020 379 Dihedral : 12.272 59.240 497 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.04 % Allowed : 19.13 % Favored : 77.83 % 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: 2.07 (0.52), residues: 266 helix: 2.80 (0.36), residues: 176 sheet: -1.68 (1.41), residues: 13 loop : -1.65 (0.69), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 670 TYR 0.015 0.002 TYR L 64 PHE 0.012 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 0.00367 / 0.15 ( 2407) covalent geometry : angle 0.62845 / 0.31 ( 3239) SS BOND : bond 0.00439 / 0.21 ( 3) SS BOND : angle 1.00833 / 0.43 ( 6) hydrogen bonds : bond 0.03917 / 2.19 ( 157) hydrogen bonds : angle 4.02449 / 2.72 ( 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 38 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.086 Fit side-chains REVERT: C 407 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.4346 (mmt90) REVERT: H 673 SER cc_start: 0.8653 (t) cc_final: 0.8342 (m) outliers start: 7 outliers final: 4 residues processed: 36 average time/residue: 0.3485 time to fit residues: 12.9758 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 : 0.083 ------------------------------------------------------------------------------- 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 C residue 416 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: 0.8980 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 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 = 0.3768 r_free = 0.3768 target = 0.127289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.094692 restraints weight = 15637.735| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 6.67 r_work: 0.2916 rms_B_bonded: 6.27 restraints_weight: 2.0000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 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 = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2410 Z= 0.155 Angle : 0.658 7.856 3245 Z= 0.323 Chirality : 0.041 0.142 355 Planarity : 0.003 0.016 379 Dihedral : 12.212 62.020 497 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.17 % Allowed : 21.30 % Favored : 76.52 % 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: 2.00 (0.52), residues: 266 helix: 2.73 (0.36), residues: 176 sheet: -1.63 (1.47), residues: 13 loop : -1.62 (0.69), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 670 TYR 0.013 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 0.00370 / 0.16 ( 2407) covalent geometry : angle 0.65748 / 0.32 ( 3239) SS BOND : bond 0.00491 / 0.23 ( 3) SS BOND : angle 0.97687 / 0.43 ( 6) hydrogen bonds : bond 0.03957 / 2.21 ( 157) hydrogen bonds : angle 4.06995 / 2.74 ( 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 37 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.085 Fit side-chains REVERT: C 407 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.4343 (mmt90) REVERT: H 673 SER cc_start: 0.8652 (t) cc_final: 0.8341 (m) outliers start: 5 outliers final: 4 residues processed: 36 average time/residue: 0.3754 time to fit residues: 14.0031 Evaluate side-chains 36 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 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 C residue 408 ILE Chi-restraints excluded: chain C residue 416 LEU 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: 0.8980 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.126653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.088242 restraints weight = 15793.517| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 5.01 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2410 Z= 0.168 Angle : 0.668 8.705 3245 Z= 0.328 Chirality : 0.041 0.145 355 Planarity : 0.003 0.017 379 Dihedral : 12.268 63.855 497 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.17 % Allowed : 21.30 % Favored : 76.52 % 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: 1.93 (0.51), residues: 266 helix: 2.67 (0.36), residues: 176 sheet: -1.64 (1.46), residues: 13 loop : -1.67 (0.69), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 670 TYR 0.016 0.002 TYR L 64 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 0.00404 / 0.17 ( 2407) covalent geometry : angle 0.66778 / 0.33 ( 3239) SS BOND : bond 0.00520 / 0.25 ( 3) SS BOND : angle 0.91781 / 0.40 ( 6) hydrogen bonds : bond 0.03987 / 2.22 ( 157) hydrogen bonds : angle 4.09606 / 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 37 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.061 Fit side-chains REVERT: C 407 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.4234 (mmt90) REVERT: H 673 SER cc_start: 0.8709 (t) cc_final: 0.8304 (m) outliers start: 5 outliers final: 3 residues processed: 36 average time/residue: 0.2900 time to fit residues: 10.7967 Evaluate side-chains 36 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.058 ------------------------------------------------------------------------------- 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 C residue 416 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 0.0170 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 9 optimal weight: 0.0970 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.128302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.090472 restraints weight = 11288.429| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 4.33 r_work: 0.3015 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2410 Z= 0.133 Angle : 0.651 9.664 3245 Z= 0.319 Chirality : 0.040 0.139 355 Planarity : 0.003 0.017 379 Dihedral : 12.046 63.509 497 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.74 % Allowed : 21.74 % Favored : 76.52 % 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: 2.13 (0.52), residues: 266 helix: 2.81 (0.36), residues: 176 sheet: -1.48 (1.50), residues: 13 loop : -1.56 (0.71), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 670 TYR 0.013 0.001 TYR L 15 PHE 0.012 0.001 PHE L 117 TRP 0.006 0.001 TRP L 130 HIS 0.001 0.001 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 2407) covalent geometry : angle 0.65092 / 0.32 ( 3239) SS BOND : bond 0.00409 / 0.20 ( 3) SS BOND : angle 0.84241 / 0.38 ( 6) hydrogen bonds : bond 0.03851 / 2.14 ( 157) hydrogen bonds : angle 4.02118 / 2.70 ( 452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 882.79 seconds wall clock time: 15 minutes 46.90 seconds (946.90 seconds total)