Starting phenix.real_space_refine on Wed Jul 1 21:05:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fan_50276/07_2026/9fan_50276.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fan_50276/07_2026/9fan_50276.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/9fan_50276/07_2026/9fan_50276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fan_50276/07_2026/9fan_50276.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fan_50276/07_2026/9fan_50276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fan_50276/07_2026/9fan_50276.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 391 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: 2348 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 472 Classifications: {'peptide': 51} Modifications used: {'COO': 1} 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: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 256 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "L" Number of atoms: 1516 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 193, 1501 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 187} Conformer: "B" Number of residues, atoms: 193, 1501 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 187} bond proxies already assigned to first conformer: 1524 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'D10': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Time building chain proxies: 1.09, per 1000 atoms: 0.46 Number of scatterers: 2348 At special positions: 0 Unit cell: (52.336, 60.2657, 85.6408, 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 391 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: 0.25 Conformation dependent library (CDL) restraints added in 126.0 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: 10 helices and 1 sheets defined 69.7% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'C' and resid 374 through 380 Processing helix chain 'C' and resid 401 through 427 removed outlier: 4.029A 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 673 through 699 Processing helix chain 'L' and resid 12 through 43 Processing helix chain 'L' and resid 89 through 113 Processing helix 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: 3.629A pdb=" N TRP L 150 " --> pdb=" O PRO L 147 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP L 151 " --> pdb=" O ASP L 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 147 through 151' Processing helix chain 'L' and resid 152 through 160 removed outlier: 3.546A pdb=" N MET L 158 " --> pdb=" O THR L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 203 removed outlier: 3.792A pdb=" N ILE L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR L 202 " --> pdb=" O GLY L 198 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 76 through 78 156 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: 0.33 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 350 1.32 - 1.45: 693 1.45 - 1.57: 1333 1.57 - 1.69: 2 1.69 - 1.82: 32 Bond restraints: 2410 Sorted by residual: bond pdb=" N ASP C 374 " pdb=" CA ASP C 374 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 6.95e+00 bond pdb=" N ILE L 106 " pdb=" CA ILE L 106 " ideal model delta sigma weight residual 1.459 1.492 -0.032 1.23e-02 6.61e+03 6.92e+00 bond pdb=" N VAL L 140 " pdb=" CA VAL L 140 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.69e+00 bond pdb=" N VAL L 104 " pdb=" CA VAL L 104 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.30e-02 5.92e+03 6.28e+00 bond pdb=" N LYS C 373 " pdb=" CA LYS C 373 " ideal model delta sigma weight residual 1.453 1.483 -0.030 1.22e-02 6.72e+03 5.93e+00 ... (remaining 2405 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 3208 3.76 - 7.51: 34 7.51 - 11.27: 0 11.27 - 15.03: 0 15.03 - 18.78: 3 Bond angle restraints: 3245 Sorted by residual: angle pdb=" CB P1L C 381 " pdb=" SG P1L C 381 " pdb=" C7 P1L C 381 " ideal model delta sigma weight residual 102.31 121.09 -18.78 3.00e+00 1.11e-01 3.92e+01 angle pdb=" CB P1L C 380 " pdb=" SG P1L C 380 " pdb=" C7 P1L C 380 " ideal model delta sigma weight residual 102.31 120.50 -18.19 3.00e+00 1.11e-01 3.68e+01 angle pdb=" CB P1L C 385 " pdb=" SG P1L C 385 " pdb=" C7 P1L C 385 " ideal model delta sigma weight residual 102.31 120.00 -17.69 3.00e+00 1.11e-01 3.48e+01 angle pdb=" CA ILE L 127 " pdb=" C ILE L 127 " pdb=" O ILE L 127 " ideal model delta sigma weight residual 121.17 116.95 4.22 1.06e+00 8.90e-01 1.58e+01 angle pdb=" CA ASP L 148 " pdb=" CB ASP L 148 " pdb=" CG ASP L 148 " ideal model delta sigma weight residual 112.60 116.48 -3.88 1.00e+00 1.00e+00 1.50e+01 ... (remaining 3240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 1433 34.98 - 69.96: 39 69.96 - 104.94: 4 104.94 - 139.92: 2 139.92 - 174.90: 1 Dihedral angle restraints: 1479 sinusoidal: 667 harmonic: 812 Sorted by residual: dihedral pdb=" C07 PGW L1002 " pdb=" C06 PGW L1002 " pdb=" C10 PGW L1002 " pdb=" C9 PGW L1002 " ideal model delta sinusoidal sigma weight residual 110.06 -64.84 174.90 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CAD PGW L1002 " pdb=" C04 PGW L1002 " pdb=" C05 PGW L1002 " pdb=" O12 PGW L1002 " ideal model delta sinusoidal sigma weight residual 168.74 59.17 109.57 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" O12 PGW L1002 " pdb=" C04 PGW L1002 " pdb=" C05 PGW L1002 " pdb=" OAF PGW L1002 " ideal model delta sinusoidal sigma weight residual 69.27 177.48 -108.21 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 1476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 303 0.071 - 0.142: 43 0.142 - 0.213: 6 0.213 - 0.284: 1 0.284 - 0.354: 2 Chirality restraints: 355 Sorted by residual: 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 2.67 -0.35 2.00e-01 2.50e+01 3.14e+00 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 2.64 -0.32 2.00e-01 2.50e+01 2.61e+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 2.56 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 352 not shown) Planarity restraints: 382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW L1002 " -0.080 2.00e-02 2.50e+03 1.55e-01 2.40e+02 pdb=" C10 PGW L1002 " 0.206 2.00e-02 2.50e+03 pdb=" C8 PGW L1002 " 0.077 2.00e-02 2.50e+03 pdb=" C9 PGW L1002 " -0.203 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA P1L C 380 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C P1L C 380 " 0.039 2.00e-02 2.50e+03 pdb=" O P1L C 380 " -0.015 2.00e-02 2.50e+03 pdb=" N P1L C 381 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA L 96 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.52e+00 pdb=" C ALA L 96 " -0.027 2.00e-02 2.50e+03 pdb=" O ALA L 96 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE L 97 " 0.009 2.00e-02 2.50e+03 ... (remaining 379 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 408 2.77 - 3.30: 2310 3.30 - 3.83: 3637 3.83 - 4.37: 4655 4.37 - 4.90: 7871 Nonbonded interactions: 18881 Sorted by model distance: nonbonded pdb=" OD1 ASN H 690 " pdb=" ND2 ASN L 186 " model vdw 2.236 3.120 nonbonded pdb=" O1 CLR C 502 " pdb="CL CL L1003 " model vdw 2.351 3.270 nonbonded pdb=" O VAL C 420 " pdb=" OG SER C 424 " model vdw 2.449 3.040 nonbonded pdb=" O ILE C 408 " pdb=" OG1 THR C 412 " model vdw 2.483 3.040 nonbonded pdb=" O PHE C 379 " pdb=" NE1 TRP L 130 " model vdw 2.505 3.120 ... (remaining 18876 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: 1.930 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.380 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:8.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 0.043 2413 Z= 0.406 Angle : 1.111 18.784 3251 Z= 0.628 Chirality : 0.058 0.354 355 Planarity : 0.009 0.155 382 Dihedral : 17.223 174.902 950 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.43 % Allowed : 1.74 % Favored : 97.83 % 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: 0.64 (0.53), residues: 266 helix: 1.46 (0.39), residues: 174 sheet: -1.13 (1.71), residues: 11 loop : -1.65 (0.72), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 17 TYR 0.013 0.001 TYR L 166 PHE 0.019 0.002 PHE H 694 TRP 0.011 0.001 TRP L 150 HIS 0.002 0.001 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.41 ( 2410) covalent geometry : angle 1.10315 / 0.63 ( 3245) SS BOND : bond 0.00478 / 0.23 ( 3) SS BOND : angle 3.22992 / 1.27 ( 6) hydrogen bonds : bond 0.14700 / 8.36 ( 156) hydrogen bonds : angle 6.32806 / 4.58 ( 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: 1 poor density : 46 time to evaluate : 0.081 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.3815 time to fit residues: 18.4663 Evaluate side-chains 39 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 186 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 = 0.3426 r_free = 0.3426 target = 0.104353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.073246 restraints weight = 18672.727| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 5.40 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2413 Z= 0.152 Angle : 0.539 4.979 3251 Z= 0.282 Chirality : 0.039 0.134 355 Planarity : 0.004 0.028 382 Dihedral : 16.034 125.551 500 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.61 % Allowed : 12.17 % 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: 1.85 (0.53), residues: 266 helix: 2.57 (0.37), residues: 176 sheet: -1.13 (1.65), residues: 11 loop : -1.71 (0.71), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 398 TYR 0.010 0.001 TYR L 15 PHE 0.012 0.001 PHE L 59 TRP 0.006 0.001 TRP C 422 HIS 0.002 0.001 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 2410) covalent geometry : angle 0.53549 / 0.28 ( 3245) SS BOND : bond 0.00436 / 0.21 ( 3) SS BOND : angle 1.59950 / 0.71 ( 6) hydrogen bonds : bond 0.04385 / 2.53 ( 156) hydrogen bonds : angle 4.20498 / 2.99 ( 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 47 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.049 Fit side-chains REVERT: C 401 LYS cc_start: 0.7381 (mtmm) cc_final: 0.7075 (mmmm) outliers start: 6 outliers final: 0 residues processed: 43 average time/residue: 0.2843 time to fit residues: 12.5752 Evaluate side-chains 40 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 186 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 = 0.3411 r_free = 0.3411 target = 0.103468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.072234 restraints weight = 18170.161| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 5.37 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2413 Z= 0.162 Angle : 0.534 5.314 3251 Z= 0.276 Chirality : 0.039 0.134 355 Planarity : 0.003 0.024 382 Dihedral : 14.931 109.980 500 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.17 % Allowed : 15.65 % 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: 2.26 (0.52), residues: 266 helix: 2.84 (0.37), residues: 177 sheet: -1.02 (1.56), residues: 11 loop : -1.43 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 398 TYR 0.009 0.001 TYR L 15 PHE 0.011 0.001 PHE L 59 TRP 0.004 0.001 TRP L 175 HIS 0.002 0.001 HIS C 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 2410) covalent geometry : angle 0.53337 / 0.28 ( 3245) SS BOND : bond 0.00494 / 0.24 ( 3) SS BOND : angle 0.91926 / 0.44 ( 6) hydrogen bonds : bond 0.04252 / 2.45 ( 156) hydrogen bonds : angle 4.01766 / 2.85 ( 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 48 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.089 Fit side-chains REVERT: C 398 ARG cc_start: 0.6938 (mtp85) cc_final: 0.6709 (ptp-170) REVERT: C 401 LYS cc_start: 0.7385 (mtmm) cc_final: 0.6917 (mmtp) outliers start: 5 outliers final: 1 residues processed: 44 average time/residue: 0.4232 time to fit residues: 19.1707 Evaluate side-chains 43 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 ASN ** L 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.103784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.071606 restraints weight = 15633.865| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 5.28 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2413 Z= 0.146 Angle : 0.535 5.347 3251 Z= 0.280 Chirality : 0.039 0.188 355 Planarity : 0.003 0.021 382 Dihedral : 14.711 109.489 500 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: 2.43 (0.53), residues: 266 helix: 2.93 (0.37), residues: 177 sheet: -0.44 (1.59), residues: 11 loop : -1.35 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 200 TYR 0.009 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 C 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 2410) covalent geometry : angle 0.52216 / 0.27 ( 3245) SS BOND : bond 0.00542 / 0.26 ( 3) SS BOND : angle 2.78543 / 1.10 ( 6) hydrogen bonds : bond 0.04281 / 2.44 ( 156) hydrogen bonds : angle 4.07386 / 2.89 ( 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 51 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.086 Fit side-chains REVERT: C 398 ARG cc_start: 0.6965 (mtp85) cc_final: 0.6416 (ptp-170) REVERT: C 401 LYS cc_start: 0.7354 (mtmm) cc_final: 0.6892 (mmtp) REVERT: H 698 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.7323 (m-10) REVERT: L 18 ASN cc_start: 0.7682 (m-40) cc_final: 0.7394 (m110) outliers start: 5 outliers final: 1 residues processed: 47 average time/residue: 0.4004 time to fit residues: 19.3768 Evaluate side-chains 45 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 698 TYR Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 0.0270 chunk 3 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 186 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 = 0.3433 r_free = 0.3433 target = 0.104838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.072841 restraints weight = 13952.440| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 5.06 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2413 Z= 0.125 Angle : 0.507 5.480 3251 Z= 0.264 Chirality : 0.037 0.146 355 Planarity : 0.003 0.021 382 Dihedral : 14.014 96.797 500 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.17 % Allowed : 19.13 % 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: 2.61 (0.52), residues: 266 helix: 3.07 (0.37), residues: 177 sheet: -0.05 (1.60), residues: 11 loop : -1.35 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 200 TYR 0.008 0.001 TYR C 421 PHE 0.011 0.001 PHE L 59 TRP 0.006 0.001 TRP L 175 HIS 0.001 0.000 HIS C 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 2410) covalent geometry : angle 0.50035 / 0.26 ( 3245) SS BOND : bond 0.00635 / 0.30 ( 3) SS BOND : angle 2.01700 / 0.79 ( 6) hydrogen bonds : bond 0.04036 / 2.30 ( 156) hydrogen bonds : angle 3.92550 / 2.77 ( 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 50 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.088 Fit side-chains REVERT: C 398 ARG cc_start: 0.6958 (mtp85) cc_final: 0.6666 (ptp-170) REVERT: C 401 LYS cc_start: 0.7332 (mtmm) cc_final: 0.6862 (mmtp) REVERT: H 698 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.7264 (m-10) REVERT: L 18 ASN cc_start: 0.7617 (m-40) cc_final: 0.7351 (m110) REVERT: L 200 ARG cc_start: 0.8135 (tpp80) cc_final: 0.7736 (ttt90) outliers start: 5 outliers final: 0 residues processed: 46 average time/residue: 0.4140 time to fit residues: 19.6389 Evaluate side-chains 43 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 698 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 21 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 186 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 = 0.3437 r_free = 0.3437 target = 0.105132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.072315 restraints weight = 20980.259| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 5.82 r_work: 0.2663 rms_B_bonded: 5.61 restraints_weight: 2.0000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2413 Z= 0.120 Angle : 0.505 5.754 3251 Z= 0.261 Chirality : 0.037 0.139 355 Planarity : 0.003 0.021 382 Dihedral : 13.216 88.625 500 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.30 % Allowed : 21.30 % Favored : 77.39 % 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: 2.70 (0.52), residues: 266 helix: 3.11 (0.37), residues: 177 sheet: -0.11 (1.40), residues: 11 loop : -1.23 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 200 TYR 0.008 0.001 TYR C 421 PHE 0.011 0.001 PHE C 379 TRP 0.007 0.001 TRP L 175 HIS 0.001 0.001 HIS C 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 2410) covalent geometry : angle 0.50143 / 0.26 ( 3245) SS BOND : bond 0.00565 / 0.27 ( 3) SS BOND : angle 1.45098 / 0.58 ( 6) hydrogen bonds : bond 0.04000 / 2.30 ( 156) hydrogen bonds : angle 3.88571 / 2.75 ( 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 47 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.085 Fit side-chains REVERT: C 398 ARG cc_start: 0.7015 (mtp85) cc_final: 0.6687 (ptp-170) REVERT: C 401 LYS cc_start: 0.7193 (mtmm) cc_final: 0.6808 (mmtp) REVERT: H 698 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.7381 (m-10) REVERT: L 18 ASN cc_start: 0.7548 (m-40) cc_final: 0.7290 (m110) REVERT: L 200 ARG cc_start: 0.8250 (tpp80) cc_final: 0.7851 (ttt90) outliers start: 3 outliers final: 1 residues processed: 45 average time/residue: 0.4099 time to fit residues: 19.0125 Evaluate side-chains 45 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 698 TYR Chi-restraints excluded: chain L residue 178 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 186 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 = 0.3406 r_free = 0.3406 target = 0.102903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.071015 restraints weight = 17377.231| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 5.32 r_work: 0.2639 rms_B_bonded: 5.32 restraints_weight: 2.0000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2413 Z= 0.154 Angle : 0.526 5.836 3251 Z= 0.273 Chirality : 0.038 0.137 355 Planarity : 0.003 0.021 382 Dihedral : 13.130 89.900 500 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.74 % Allowed : 21.30 % Favored : 76.96 % 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: 2.66 (0.52), residues: 266 helix: 3.14 (0.37), residues: 176 sheet: 0.01 (1.39), residues: 11 loop : -1.39 (0.69), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 200 TYR 0.009 0.001 TYR C 421 PHE 0.013 0.001 PHE C 378 TRP 0.005 0.001 TRP L 130 HIS 0.001 0.001 HIS C 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 2410) covalent geometry : angle 0.52317 / 0.27 ( 3245) SS BOND : bond 0.00684 / 0.33 ( 3) SS BOND : angle 1.33465 / 0.54 ( 6) hydrogen bonds : bond 0.04225 / 2.44 ( 156) hydrogen bonds : angle 3.96394 / 2.81 ( 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 45 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.076 Fit side-chains REVERT: C 398 ARG cc_start: 0.7041 (mtp85) cc_final: 0.6703 (ptp-170) REVERT: C 401 LYS cc_start: 0.7271 (mtmm) cc_final: 0.6869 (mmtp) REVERT: H 698 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7333 (m-10) REVERT: L 18 ASN cc_start: 0.7616 (m-40) cc_final: 0.7339 (m110) REVERT: L 200 ARG cc_start: 0.8264 (tpp80) cc_final: 0.7860 (ttt90) outliers start: 4 outliers final: 1 residues processed: 43 average time/residue: 0.3941 time to fit residues: 17.4512 Evaluate side-chains 41 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 698 TYR Chi-restraints excluded: chain L residue 178 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 19 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 186 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 = 0.3433 r_free = 0.3433 target = 0.104815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.072633 restraints weight = 14437.229| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 5.05 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2413 Z= 0.122 Angle : 0.497 5.950 3251 Z= 0.259 Chirality : 0.037 0.137 355 Planarity : 0.003 0.021 382 Dihedral : 12.443 87.335 500 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.30 % Allowed : 21.74 % Favored : 76.96 % 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: 2.77 (0.52), residues: 266 helix: 3.23 (0.37), residues: 176 sheet: -0.06 (1.39), residues: 11 loop : -1.31 (0.69), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 200 TYR 0.008 0.001 TYR C 421 PHE 0.011 0.001 PHE L 59 TRP 0.007 0.001 TRP L 175 HIS 0.001 0.000 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 2410) covalent geometry : angle 0.49481 / 0.26 ( 3245) SS BOND : bond 0.00524 / 0.25 ( 3) SS BOND : angle 1.08654 / 0.46 ( 6) hydrogen bonds : bond 0.04023 / 2.34 ( 156) hydrogen bonds : angle 3.88754 / 2.76 ( 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 47 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.054 Fit side-chains REVERT: C 398 ARG cc_start: 0.6923 (mtp85) cc_final: 0.6522 (ptp-170) REVERT: C 401 LYS cc_start: 0.7363 (mtmm) cc_final: 0.6885 (mmtp) REVERT: H 698 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.7396 (m-10) REVERT: L 18 ASN cc_start: 0.7659 (m-40) cc_final: 0.7352 (m110) REVERT: L 200 ARG cc_start: 0.8172 (tpp80) cc_final: 0.7754 (ttt90) outliers start: 3 outliers final: 1 residues processed: 44 average time/residue: 0.3528 time to fit residues: 15.9728 Evaluate side-chains 43 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 698 TYR Chi-restraints excluded: chain L residue 178 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 186 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 = 0.3440 r_free = 0.3440 target = 0.105138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.073450 restraints weight = 15521.289| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 5.12 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2413 Z= 0.128 Angle : 0.512 6.107 3251 Z= 0.265 Chirality : 0.037 0.137 355 Planarity : 0.003 0.020 382 Dihedral : 12.204 87.055 500 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.30 % Allowed : 22.61 % Favored : 76.09 % 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: 2.78 (0.52), residues: 266 helix: 3.17 (0.37), residues: 177 sheet: 0.10 (1.40), residues: 11 loop : -1.22 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 200 TYR 0.009 0.001 TYR C 421 PHE 0.011 0.001 PHE C 378 TRP 0.006 0.001 TRP L 175 HIS 0.001 0.000 HIS C 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 2410) covalent geometry : angle 0.51086 / 0.26 ( 3245) SS BOND : bond 0.00547 / 0.26 ( 3) SS BOND : angle 0.93496 / 0.40 ( 6) hydrogen bonds : bond 0.04065 / 2.36 ( 156) hydrogen bonds : angle 3.90563 / 2.76 ( 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 43 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.054 Fit side-chains revert: symmetry clash REVERT: C 401 LYS cc_start: 0.7326 (mtmm) cc_final: 0.6982 (mmmm) REVERT: H 698 TYR cc_start: 0.7818 (OUTLIER) cc_final: 0.7314 (m-10) REVERT: L 18 ASN cc_start: 0.7663 (m-40) cc_final: 0.7356 (m110) REVERT: L 200 ARG cc_start: 0.8127 (tpp80) cc_final: 0.7696 (ttt90) outliers start: 3 outliers final: 1 residues processed: 40 average time/residue: 0.3208 time to fit residues: 13.2003 Evaluate side-chains 41 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 698 TYR Chi-restraints excluded: chain L residue 178 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 186 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 = 0.3429 r_free = 0.3429 target = 0.104236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.071843 restraints weight = 22397.480| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 6.25 r_work: 0.2641 rms_B_bonded: 5.70 restraints_weight: 2.0000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2413 Z= 0.135 Angle : 0.514 6.127 3251 Z= 0.266 Chirality : 0.038 0.136 355 Planarity : 0.003 0.020 382 Dihedral : 12.073 87.306 500 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.30 % Allowed : 23.48 % Favored : 75.22 % 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: 2.74 (0.52), residues: 266 helix: 3.13 (0.37), residues: 177 sheet: 0.12 (1.39), residues: 11 loop : -1.24 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 200 TYR 0.009 0.001 TYR C 421 PHE 0.011 0.001 PHE L 59 TRP 0.006 0.001 TRP L 175 HIS 0.001 0.001 HIS C 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 2410) covalent geometry : angle 0.51308 / 0.27 ( 3245) SS BOND : bond 0.00536 / 0.26 ( 3) SS BOND : angle 0.90209 / 0.38 ( 6) hydrogen bonds : bond 0.04096 / 2.38 ( 156) hydrogen bonds : angle 3.91590 / 2.77 ( 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 42 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: C 401 LYS cc_start: 0.7194 (mtmm) cc_final: 0.6956 (mmmm) REVERT: H 698 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.7372 (m-10) REVERT: L 18 ASN cc_start: 0.7545 (m-40) cc_final: 0.7273 (m110) REVERT: L 200 ARG cc_start: 0.8241 (tpp80) cc_final: 0.7829 (ttt90) outliers start: 3 outliers final: 1 residues processed: 39 average time/residue: 0.4332 time to fit residues: 17.3653 Evaluate side-chains 41 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 698 TYR Chi-restraints excluded: chain L residue 178 ILE 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 22 optimal weight: 0.1980 chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 186 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 = 0.3421 r_free = 0.3421 target = 0.103600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.070624 restraints weight = 18117.241| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 5.48 r_work: 0.2650 rms_B_bonded: 5.42 restraints_weight: 2.0000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2413 Z= 0.141 Angle : 0.521 6.159 3251 Z= 0.269 Chirality : 0.038 0.135 355 Planarity : 0.003 0.020 382 Dihedral : 11.995 87.592 500 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.87 % Allowed : 23.48 % Favored : 75.65 % 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: 2.68 (0.51), residues: 266 helix: 3.09 (0.36), residues: 177 sheet: 0.04 (1.36), residues: 11 loop : -1.25 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 200 TYR 0.009 0.001 TYR C 421 PHE 0.011 0.001 PHE L 59 TRP 0.005 0.001 TRP L 175 HIS 0.001 0.001 HIS C 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 2410) covalent geometry : angle 0.51953 / 0.27 ( 3245) SS BOND : bond 0.00549 / 0.26 ( 3) SS BOND : angle 0.91676 / 0.39 ( 6) hydrogen bonds : bond 0.04146 / 2.41 ( 156) hydrogen bonds : angle 3.94406 / 2.79 ( 452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 891.02 seconds wall clock time: 15 minutes 55.04 seconds (955.04 seconds total)