Starting phenix.real_space_refine on Tue Aug 4 12:07:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fan_50276/08_2026/9fan_50276.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fan_50276/08_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_50276/08_2026/9fan_50276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fan_50276/08_2026/9fan_50276.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fan_50276/08_2026/9fan_50276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fan_50276/08_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-2.2rc3-6140/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, 62 Unusual residues: {' CL': 1, 'D10': 1, 'PGW': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.05, per 1000 atoms: 0.45 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: 0.27 Conformation dependent library (CDL) restraints added in 137.3 milliseconds 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 520 Finding SS restraints... Secondary structure from input PDB file: 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: 0.38 Time building geometry restraints manager: 0.34 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 3.190 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: 2.260 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.240 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.140 ------------------------------------------------------------------------------- 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 : 0.053 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.3892 time to fit residues: 18.8064 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 : 0.079 ------------------------------------------------------------------------------- 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: 0.8980 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 = 0.3435 r_free = 0.3435 target = 0.104337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.071822 restraints weight = 19205.270| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 5.71 r_work: 0.2671 rms_B_bonded: 5.65 restraints_weight: 2.0000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2413 Z= 0.153 Angle : 0.543 5.047 3251 Z= 0.283 Chirality : 0.039 0.130 355 Planarity : 0.004 0.028 382 Dihedral : 15.867 123.260 500 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 : 11.74 % Favored : 85.65 % 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: 1.85 (0.53), residues: 266 helix: 2.52 (0.37), residues: 177 sheet: -1.13 (1.65), residues: 11 loop : -1.59 (0.71), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 398 TYR 0.009 0.001 TYR L 15 PHE 0.012 0.001 PHE L 59 TRP 0.007 0.001 TRP C 422 HIS 0.002 0.001 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 2410) covalent geometry : angle 0.53886 / 0.28 ( 3245) SS BOND : bond 0.00498 / 0.24 ( 3) SS BOND : angle 1.61499 / 0.71 ( 6) hydrogen bonds : bond 0.04363 / 2.51 ( 156) hydrogen bonds : angle 4.19792 / 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 48 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.130 Fit side-chains REVERT: C 401 LYS cc_start: 0.7182 (mtmm) cc_final: 0.6967 (mmmm) outliers start: 6 outliers final: 0 residues processed: 44 average time/residue: 0.4449 time to fit residues: 20.1617 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 : 0.067 ------------------------------------------------------------------------------- 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: 3.9990 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 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 = 0.3407 r_free = 0.3407 target = 0.103200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.071976 restraints weight = 18224.133| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 5.36 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2197 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= 0.161 Angle : 0.537 5.297 3251 Z= 0.276 Chirality : 0.039 0.135 355 Planarity : 0.003 0.024 382 Dihedral : 14.950 109.634 500 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.04 % Allowed : 15.22 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.52), residues: 266 helix: 2.83 (0.37), residues: 177 sheet: -1.01 (1.56), residues: 11 loop : -1.39 (0.71), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 20 TYR 0.010 0.001 TYR L 15 PHE 0.011 0.001 PHE L 59 TRP 0.004 0.001 TRP L 175 HIS 0.002 0.000 HIS C 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 2410) covalent geometry : angle 0.53570 / 0.28 ( 3245) SS BOND : bond 0.00481 / 0.23 ( 3) SS BOND : angle 0.94241 / 0.44 ( 6) hydrogen bonds : bond 0.04264 / 2.45 ( 156) hydrogen bonds : angle 4.02104 / 2.86 ( 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 49 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.054 Fit side-chains REVERT: C 398 ARG cc_start: 0.6919 (mtp85) cc_final: 0.6714 (ptp-170) REVERT: C 401 LYS cc_start: 0.7402 (mtmm) cc_final: 0.6933 (mmtp) REVERT: H 698 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7162 (m-10) REVERT: L 18 ASN cc_start: 0.7719 (m110) cc_final: 0.7445 (m110) outliers start: 7 outliers final: 1 residues processed: 44 average time/residue: 0.4243 time to fit residues: 19.2133 Evaluate side-chains 44 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 698 TYR 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: 0.5980 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 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 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 = 0.103662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.072738 restraints weight = 15520.564| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 5.15 r_work (final): 0.2888 ------------------------------------------------------------------------------- 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 = 0.45 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 = 0.46 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: 0.8638 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2413 Z= 0.144 Angle : 0.535 5.378 3251 Z= 0.279 Chirality : 0.039 0.185 355 Planarity : 0.003 0.021 382 Dihedral : 14.640 108.159 500 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.17 % Allowed : 18.70 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.53), residues: 266 helix: 2.95 (0.37), residues: 177 sheet: -0.46 (1.59), residues: 11 loop : -1.34 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 200 TYR 0.009 0.001 TYR L 15 PHE 0.011 0.001 PHE L 59 TRP 0.008 0.001 TRP L 130 HIS 0.001 0.001 HIS C 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 2410) covalent geometry : angle 0.52358 / 0.27 ( 3245) SS BOND : bond 0.00576 / 0.28 ( 3) SS BOND : angle 2.61716 / 1.03 ( 6) hydrogen bonds : bond 0.04266 / 2.43 ( 156) hydrogen bonds : angle 4.05495 / 2.87 ( 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 : 0.113 Fit side-chains REVERT: C 398 ARG cc_start: 0.6967 (mtp85) cc_final: 0.6664 (ptp-170) REVERT: C 401 LYS cc_start: 0.7365 (mtmm) cc_final: 0.6899 (mmtp) REVERT: H 698 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7299 (m-10) outliers start: 5 outliers final: 1 residues processed: 47 average time/residue: 0.3903 time to fit residues: 18.9252 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 : 0.086 ------------------------------------------------------------------------------- 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: 0.5980 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 0.0170 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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 = 0.104267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.073287 restraints weight = 14009.786| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 4.97 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2413 Z= 0.126 Angle : 0.508 5.402 3251 Z= 0.264 Chirality : 0.037 0.140 355 Planarity : 0.003 0.020 382 Dihedral : 13.939 93.599 500 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.17 % Allowed : 19.57 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.52), residues: 266 helix: 3.06 (0.37), residues: 177 sheet: -0.13 (1.60), residues: 11 loop : -1.34 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 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 130 HIS 0.001 0.000 HIS C 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 2410) covalent geometry : angle 0.50174 / 0.26 ( 3245) SS BOND : bond 0.00669 / 0.32 ( 3) SS BOND : angle 1.97804 / 0.77 ( 6) hydrogen bonds : bond 0.04038 / 2.31 ( 156) hydrogen bonds : angle 3.92850 / 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 : 0.102 Fit side-chains REVERT: C 398 ARG cc_start: 0.6959 (mtp85) cc_final: 0.6663 (ptp-170) REVERT: C 401 LYS cc_start: 0.7337 (mtmm) cc_final: 0.6865 (mmtp) REVERT: H 698 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.7673 (m-10) REVERT: L 18 ASN cc_start: 0.7607 (m110) cc_final: 0.7351 (m110) REVERT: L 200 ARG cc_start: 0.8131 (tpp80) cc_final: 0.7704 (ttt90) outliers start: 5 outliers final: 0 residues processed: 46 average time/residue: 0.3963 time to fit residues: 18.7650 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 : 0.083 ------------------------------------------------------------------------------- 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: 0.5980 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 3 optimal weight: 0.2980 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 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 = 0.3409 r_free = 0.3409 target = 0.102925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.071183 restraints weight = 21121.255| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 5.67 r_work: 0.2639 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2413 Z= 0.149 Angle : 0.532 5.731 3251 Z= 0.274 Chirality : 0.038 0.138 355 Planarity : 0.003 0.020 382 Dihedral : 13.585 89.479 500 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.61 % Allowed : 19.57 % 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: 2.57 (0.52), residues: 266 helix: 3.01 (0.37), residues: 177 sheet: -0.21 (1.38), residues: 11 loop : -1.28 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 200 TYR 0.009 0.001 TYR C 421 PHE 0.014 0.001 PHE C 378 TRP 0.006 0.001 TRP L 175 HIS 0.002 0.001 HIS C 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 2410) covalent geometry : angle 0.52800 / 0.27 ( 3245) SS BOND : bond 0.00687 / 0.33 ( 3) SS BOND : angle 1.56641 / 0.63 ( 6) hydrogen bonds : bond 0.04182 / 2.39 ( 156) hydrogen bonds : angle 3.96269 / 2.81 ( 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 49 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.086 Fit side-chains REVERT: C 398 ARG cc_start: 0.7051 (mtp85) cc_final: 0.6701 (ptp-170) REVERT: C 401 LYS cc_start: 0.7235 (mtmm) cc_final: 0.6842 (mmtp) REVERT: H 698 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.7254 (m-10) REVERT: L 18 ASN cc_start: 0.7585 (m-40) cc_final: 0.7290 (m110) REVERT: L 200 ARG cc_start: 0.8278 (tpp80) cc_final: 0.7877 (ttt90) outliers start: 6 outliers final: 1 residues processed: 45 average time/residue: 0.3735 time to fit residues: 17.3294 Evaluate side-chains 44 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.086 ------------------------------------------------------------------------------- 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: 0.6980 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 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 = 0.3400 r_free = 0.3400 target = 0.102248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.070582 restraints weight = 17515.756| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 5.33 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2413 Z= 0.154 Angle : 0.531 5.748 3251 Z= 0.276 Chirality : 0.038 0.137 355 Planarity : 0.003 0.021 382 Dihedral : 13.191 89.724 500 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.17 % Allowed : 20.87 % 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: 2.58 (0.52), residues: 266 helix: 3.04 (0.37), residues: 177 sheet: -0.25 (1.33), residues: 11 loop : -1.31 (0.69), residues: 78 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 0.014 0.001 PHE C 378 TRP 0.005 0.001 TRP L 175 HIS 0.001 0.000 HIS C 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 2410) covalent geometry : angle 0.52859 / 0.28 ( 3245) SS BOND : bond 0.00601 / 0.29 ( 3) SS BOND : angle 1.37962 / 0.56 ( 6) hydrogen bonds : bond 0.04245 / 2.46 ( 156) hydrogen bonds : angle 3.96570 / 2.80 ( 452) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.052 Fit side-chains REVERT: C 398 ARG cc_start: 0.7011 (mtp85) cc_final: 0.6695 (ptp-170) REVERT: C 401 LYS cc_start: 0.7403 (mtmm) cc_final: 0.6915 (mmtp) REVERT: H 698 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.7292 (m-10) REVERT: L 18 ASN cc_start: 0.7676 (m-40) cc_final: 0.7395 (m110) REVERT: L 200 ARG cc_start: 0.8179 (tpp80) cc_final: 0.7781 (ttt90) outliers start: 5 outliers final: 2 residues processed: 43 average time/residue: 0.3122 time to fit residues: 13.8182 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 : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 698 TYR Chi-restraints excluded: chain L residue 168 LEU 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: 0.0270 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.103614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.072204 restraints weight = 14468.500| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 5.01 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 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 = 0.2878 r_free = 0.2878 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: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2413 Z= 0.129 Angle : 0.509 5.965 3251 Z= 0.265 Chirality : 0.037 0.137 355 Planarity : 0.003 0.021 382 Dihedral : 12.524 86.869 500 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: 3.13 (0.37), residues: 177 sheet: -0.11 (1.40), residues: 11 loop : -1.28 (0.70), residues: 78 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 C 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 2410) covalent geometry : angle 0.50702 / 0.26 ( 3245) SS BOND : bond 0.00518 / 0.25 ( 3) SS BOND : angle 1.07661 / 0.45 ( 6) hydrogen bonds : bond 0.04082 / 2.37 ( 156) hydrogen bonds : angle 3.89619 / 2.75 ( 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 45 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.088 Fit side-chains REVERT: C 398 ARG cc_start: 0.6898 (mtp85) cc_final: 0.6506 (ptp-170) REVERT: C 401 LYS cc_start: 0.7366 (mtmm) cc_final: 0.6889 (mmtp) REVERT: H 698 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.7364 (m-10) REVERT: L 18 ASN cc_start: 0.7657 (m-40) cc_final: 0.7358 (m110) REVERT: L 200 ARG cc_start: 0.8171 (tpp80) cc_final: 0.7744 (ttt90) outliers start: 3 outliers final: 2 residues processed: 42 average time/residue: 0.3136 time to fit residues: 13.6059 Evaluate side-chains 44 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 698 TYR Chi-restraints excluded: chain L residue 168 LEU 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: 0.6980 chunk 3 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 0.0770 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.103884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.071672 restraints weight = 15704.789| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 5.22 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 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 = 0.2869 r_free = 0.2869 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: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2413 Z= 0.127 Angle : 0.511 6.006 3251 Z= 0.264 Chirality : 0.037 0.136 355 Planarity : 0.003 0.021 382 Dihedral : 12.091 85.514 500 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.04 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: 2.73 (0.52), residues: 266 helix: 3.15 (0.37), residues: 177 sheet: 0.03 (1.42), residues: 11 loop : -1.29 (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 0.010 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 0.00286 / 0.13 ( 2410) covalent geometry : angle 0.50945 / 0.26 ( 3245) SS BOND : bond 0.00478 / 0.23 ( 3) SS BOND : angle 1.00695 / 0.42 ( 6) hydrogen bonds : bond 0.04049 / 2.35 ( 156) hydrogen bonds : angle 3.86309 / 2.72 ( 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 46 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.052 Fit side-chains revert: symmetry clash REVERT: C 401 LYS cc_start: 0.7380 (mtmm) cc_final: 0.7020 (mmmm) REVERT: H 698 TYR cc_start: 0.7803 (m-80) cc_final: 0.7410 (m-10) REVERT: L 18 ASN cc_start: 0.7634 (m-40) cc_final: 0.7356 (m110) REVERT: L 200 ARG cc_start: 0.8141 (tpp80) cc_final: 0.7709 (ttt90) outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.3412 time to fit residues: 15.0893 Evaluate side-chains 40 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 6 optimal weight: 0.0980 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 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 = 0.3423 r_free = 0.3423 target = 0.103965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.072026 restraints weight = 22304.940| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 5.75 r_work: 0.2652 rms_B_bonded: 5.59 restraints_weight: 2.0000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 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 = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2413 Z= 0.122 Angle : 0.505 6.182 3251 Z= 0.262 Chirality : 0.037 0.136 355 Planarity : 0.003 0.021 382 Dihedral : 11.902 85.142 500 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.43 % Allowed : 23.04 % 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: 2.78 (0.52), residues: 266 helix: 3.18 (0.37), residues: 177 sheet: 0.19 (1.41), residues: 11 loop : -1.28 (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 0.010 0.001 PHE L 59 TRP 0.008 0.001 TRP L 175 HIS 0.001 0.000 HIS L 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 2410) covalent geometry : angle 0.50378 / 0.26 ( 3245) SS BOND : bond 0.00461 / 0.22 ( 3) SS BOND : angle 0.93490 / 0.40 ( 6) hydrogen bonds : bond 0.04029 / 2.34 ( 156) hydrogen bonds : angle 3.88047 / 2.73 ( 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: 1 poor density : 41 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: C 401 LYS cc_start: 0.7249 (mtmm) cc_final: 0.6994 (mmmm) REVERT: H 698 TYR cc_start: 0.7817 (m-80) cc_final: 0.7446 (m-10) REVERT: L 18 ASN cc_start: 0.7557 (m-40) cc_final: 0.7308 (m110) REVERT: L 200 ARG cc_start: 0.8257 (tpp80) cc_final: 0.7838 (ttt90) outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 0.4189 time to fit residues: 17.6803 Evaluate side-chains 41 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 22 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3412 r_free = 0.3412 target = 0.103005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.071424 restraints weight = 18120.073| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 5.38 r_work: 0.2650 rms_B_bonded: 5.35 restraints_weight: 2.0000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 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: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2909 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= 0.143 Angle : 0.522 6.179 3251 Z= 0.270 Chirality : 0.038 0.135 355 Planarity : 0.003 0.020 382 Dihedral : 11.957 86.279 500 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: 2.69 (0.52), residues: 266 helix: 3.11 (0.37), residues: 177 sheet: 0.10 (1.39), residues: 11 loop : -1.29 (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 0.00330 / 0.14 ( 2410) covalent geometry : angle 0.52127 / 0.27 ( 3245) SS BOND : bond 0.00541 / 0.26 ( 3) SS BOND : angle 0.96716 / 0.41 ( 6) hydrogen bonds : bond 0.04124 / 2.39 ( 156) hydrogen bonds : angle 3.91681 / 2.76 ( 452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 952.24 seconds wall clock time: 16 minutes 57.58 seconds (1017.58 seconds total)