Starting phenix.real_space_refine on Wed Jul 23 08:19:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fan_50276/07_2025/9fan_50276.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fan_50276/07_2025/9fan_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9fan_50276/07_2025/9fan_50276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fan_50276/07_2025/9fan_50276.map" model { file = "/net/cci-nas-00/data/ceres_data/9fan_50276/07_2025/9fan_50276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fan_50276/07_2025/9fan_50276.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 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: 3.50, per 1000 atoms: 1.49 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: 0.84 Conformation dependent library (CDL) restraints added in 451.6 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: 0.24 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: 0.70 Time building geometry restraints manager: 0.96 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 - 3.00: 3145 3.00 - 6.00: 92 6.00 - 9.00: 2 9.00 - 12.00: 3 12.00 - 14.99: 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 106.10 121.09 -14.99 3.00e+00 1.11e-01 2.50e+01 angle pdb=" CB P1L C 380 " pdb=" SG P1L C 380 " pdb=" C7 P1L C 380 " ideal model delta sigma weight residual 106.10 120.50 -14.40 3.00e+00 1.11e-01 2.31e+01 angle pdb=" CB P1L C 385 " pdb=" SG P1L C 385 " pdb=" C7 P1L C 385 " ideal model delta sigma weight residual 106.10 120.00 -13.90 3.00e+00 1.11e-01 2.15e+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: 1422 34.98 - 69.96: 31 69.96 - 104.94: 2 104.94 - 139.92: 2 139.92 - 174.90: 1 Dihedral angle restraints: 1458 sinusoidal: 646 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 1455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 313 0.081 - 0.161: 38 0.161 - 0.242: 1 0.242 - 0.322: 1 0.322 - 0.403: 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 2.27 2.67 -0.40 2.00e-01 2.50e+01 4.06e+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 2.27 2.64 -0.37 2.00e-01 2.50e+01 3.45e+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 2.27 2.56 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 352 not shown) Planarity restraints: 379 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 376 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: 2.050 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 13.300 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:14.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 0.047 2413 Z= 0.404 Angle : 1.156 14.994 3251 Z= 0.637 Chirality : 0.060 0.403 355 Planarity : 0.009 0.155 379 Dihedral : 16.192 174.902 929 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP L 150 HIS 0.002 0.001 HIS L 14 PHE 0.019 0.002 PHE H 694 TYR 0.013 0.001 TYR L 166 ARG 0.001 0.000 ARG L 17 Details of bonding type rmsd hydrogen bonds : bond 0.14700 ( 156) hydrogen bonds : angle 6.32806 ( 452) SS BOND : bond 0.00478 ( 3) SS BOND : angle 3.22992 ( 6) covalent geometry : bond 0.00683 ( 2410) covalent geometry : angle 1.14856 ( 3245) *********************** 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 : 0.231 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.9007 time to fit residues: 43.6550 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 : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 11 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3442 r_free = 0.3442 target = 0.104860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.072777 restraints weight = 15796.317| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 5.33 r_work (final): 0.2901 ------------------------------------------------------------------------------- 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 = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1767 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 : 0.551 4.953 3251 Z= 0.284 Chirality : 0.039 0.145 355 Planarity : 0.004 0.028 379 Dihedral : 13.832 123.128 479 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.17 % Allowed : 12.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.53), residues: 266 helix: 2.57 (0.37), residues: 176 sheet: -1.11 (1.66), residues: 11 loop : -1.68 (0.71), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 422 HIS 0.002 0.001 HIS L 14 PHE 0.012 0.001 PHE L 59 TYR 0.009 0.001 TYR L 15 ARG 0.005 0.001 ARG C 398 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 156) hydrogen bonds : angle 4.18774 ( 452) SS BOND : bond 0.00541 ( 3) SS BOND : angle 1.56336 ( 6) covalent geometry : bond 0.00328 ( 2410) covalent geometry : angle 0.54737 ( 3245) *********************** 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: 5 poor density : 42 time to evaluate : 0.236 Fit side-chains REVERT: C 401 LYS cc_start: 0.7373 (mtmm) cc_final: 0.7003 (mmtp) outliers start: 5 outliers final: 0 residues processed: 43 average time/residue: 0.9005 time to fit residues: 39.9187 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 : 0.225 ------------------------------------------------------------------------------- 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: 4.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3397 r_free = 0.3397 target = 0.102292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.069375 restraints weight = 17217.119| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 5.39 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2236 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= 0.186 Angle : 0.571 5.266 3251 Z= 0.291 Chirality : 0.040 0.140 355 Planarity : 0.003 0.024 379 Dihedral : 13.102 111.118 479 Min Nonbonded Distance : 2.561 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.53), residues: 266 helix: 2.79 (0.37), residues: 177 sheet: -1.07 (1.55), residues: 11 loop : -1.40 (0.71), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 422 HIS 0.002 0.001 HIS C 396 PHE 0.012 0.001 PHE L 59 TYR 0.010 0.001 TYR L 177 ARG 0.003 0.000 ARG L 20 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 156) hydrogen bonds : angle 4.10281 ( 452) SS BOND : bond 0.00496 ( 3) SS BOND : angle 1.02289 ( 6) covalent geometry : bond 0.00440 ( 2410) covalent geometry : angle 0.56948 ( 3245) *********************** 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 50 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.251 Fit side-chains REVERT: C 398 ARG cc_start: 0.6974 (mtp85) cc_final: 0.6718 (ptp-170) REVERT: C 401 LYS cc_start: 0.7403 (mtmm) cc_final: 0.6922 (mmtp) REVERT: H 698 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.7227 (m-10) outliers start: 7 outliers final: 1 residues processed: 45 average time/residue: 0.7729 time to fit residues: 36.0270 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 : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain H residue 698 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3410 r_free = 0.3410 target = 0.103204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.071991 restraints weight = 13594.796| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 4.95 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2416 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= 0.147 Angle : 0.546 5.303 3251 Z= 0.282 Chirality : 0.039 0.184 355 Planarity : 0.003 0.020 379 Dihedral : 12.696 112.194 479 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.53), residues: 266 helix: 2.92 (0.37), residues: 177 sheet: -0.59 (1.60), residues: 11 loop : -1.38 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 130 HIS 0.002 0.001 HIS C 396 PHE 0.011 0.001 PHE L 59 TYR 0.009 0.001 TYR L 15 ARG 0.004 0.001 ARG L 200 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 156) hydrogen bonds : angle 4.08257 ( 452) SS BOND : bond 0.00789 ( 3) SS BOND : angle 2.76362 ( 6) covalent geometry : bond 0.00337 ( 2410) covalent geometry : angle 0.53384 ( 3245) *********************** 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 49 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.254 Fit side-chains REVERT: C 398 ARG cc_start: 0.7034 (mtp85) cc_final: 0.6480 (ptp-170) REVERT: C 401 LYS cc_start: 0.7341 (mtmm) cc_final: 0.6879 (mmtp) REVERT: H 698 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.7277 (m-10) REVERT: L 18 ASN cc_start: 0.7694 (m-40) cc_final: 0.7391 (m110) outliers start: 5 outliers final: 2 residues processed: 45 average time/residue: 0.9106 time to fit residues: 42.3485 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 : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LEU 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 24 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3420 r_free = 0.3420 target = 0.103671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.072018 restraints weight = 20331.665| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 5.63 r_work: 0.2648 rms_B_bonded: 5.54 restraints_weight: 2.0000 r_work (final): 0.2648 ------------------------------------------------------------------------------- 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 = 0.45 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 = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2533 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= 0.135 Angle : 0.534 5.573 3251 Z= 0.274 Chirality : 0.038 0.149 355 Planarity : 0.003 0.020 379 Dihedral : 12.326 106.075 479 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.61 % Allowed : 18.70 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.52), residues: 266 helix: 2.99 (0.37), residues: 177 sheet: -0.35 (1.57), residues: 11 loop : -1.28 (0.71), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 175 HIS 0.001 0.000 HIS C 396 PHE 0.011 0.001 PHE L 59 TYR 0.009 0.001 TYR C 421 ARG 0.004 0.000 ARG L 200 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 156) hydrogen bonds : angle 3.98883 ( 452) SS BOND : bond 0.00656 ( 3) SS BOND : angle 2.08782 ( 6) covalent geometry : bond 0.00307 ( 2410) covalent geometry : angle 0.52676 ( 3245) *********************** 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 49 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.343 Fit side-chains REVERT: C 398 ARG cc_start: 0.7012 (mtp85) cc_final: 0.6446 (ptp-170) REVERT: C 401 LYS cc_start: 0.7210 (mtmm) cc_final: 0.6818 (mmtp) REVERT: H 698 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.7244 (m-10) REVERT: L 18 ASN cc_start: 0.7561 (m-40) cc_final: 0.7317 (m110) REVERT: L 200 ARG cc_start: 0.8244 (tpp80) cc_final: 0.7833 (ttt90) outliers start: 6 outliers final: 4 residues processed: 45 average time/residue: 0.8869 time to fit residues: 41.3249 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 : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 426 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3403 r_free = 0.3403 target = 0.102587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.070553 restraints weight = 23058.550| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 5.82 r_work: 0.2622 rms_B_bonded: 5.59 restraints_weight: 2.0000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2649 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= 0.153 Angle : 0.546 5.722 3251 Z= 0.281 Chirality : 0.039 0.144 355 Planarity : 0.003 0.020 379 Dihedral : 11.682 90.677 479 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.61 % Allowed : 20.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.52), residues: 266 helix: 3.08 (0.37), residues: 176 sheet: -0.52 (1.41), residues: 11 loop : -1.45 (0.69), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 130 HIS 0.002 0.001 HIS C 396 PHE 0.011 0.001 PHE L 59 TYR 0.009 0.001 TYR C 421 ARG 0.003 0.000 ARG L 200 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 156) hydrogen bonds : angle 3.96613 ( 452) SS BOND : bond 0.00610 ( 3) SS BOND : angle 1.60973 ( 6) covalent geometry : bond 0.00354 ( 2410) covalent geometry : angle 0.54248 ( 3245) *********************** 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: 6 poor density : 41 time to evaluate : 0.255 Fit side-chains REVERT: C 398 ARG cc_start: 0.7049 (mtp85) cc_final: 0.6708 (ptp-170) REVERT: C 401 LYS cc_start: 0.7259 (mtmm) cc_final: 0.6866 (mmtp) REVERT: H 698 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.7261 (m-10) REVERT: L 18 ASN cc_start: 0.7617 (m-40) cc_final: 0.7334 (m110) REVERT: L 200 ARG cc_start: 0.8278 (tpp80) cc_final: 0.7876 (ttt90) outliers start: 6 outliers final: 3 residues processed: 42 average time/residue: 0.8590 time to fit residues: 37.2755 Evaluate side-chains 44 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.0970 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3414 r_free = 0.3414 target = 0.103188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.070315 restraints weight = 18803.347| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 5.60 r_work: 0.2638 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2735 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= 0.139 Angle : 0.524 5.769 3251 Z= 0.270 Chirality : 0.038 0.144 355 Planarity : 0.003 0.021 379 Dihedral : 10.892 88.747 479 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.74 % Allowed : 20.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.52), residues: 266 helix: 3.17 (0.37), residues: 176 sheet: -0.62 (1.39), residues: 11 loop : -1.45 (0.69), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 175 HIS 0.001 0.000 HIS C 396 PHE 0.011 0.001 PHE L 59 TYR 0.009 0.001 TYR C 421 ARG 0.004 0.000 ARG L 200 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 156) hydrogen bonds : angle 3.90427 ( 452) SS BOND : bond 0.00583 ( 3) SS BOND : angle 1.24632 ( 6) covalent geometry : bond 0.00318 ( 2410) covalent geometry : angle 0.52186 ( 3245) *********************** 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 : 0.253 Fit side-chains REVERT: C 398 ARG cc_start: 0.6986 (mtp85) cc_final: 0.6666 (ptp-170) REVERT: C 401 LYS cc_start: 0.7227 (mtmm) cc_final: 0.6843 (mmmm) REVERT: H 698 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.7317 (m-10) REVERT: L 18 ASN cc_start: 0.7587 (m-40) cc_final: 0.7314 (m110) REVERT: L 200 ARG cc_start: 0.8277 (tpp80) cc_final: 0.7854 (ttt90) outliers start: 4 outliers final: 3 residues processed: 41 average time/residue: 0.9647 time to fit residues: 40.8034 Evaluate side-chains 44 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LEU 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 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3397 r_free = 0.3397 target = 0.102018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.070259 restraints weight = 19967.251| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 5.54 r_work: 0.2621 rms_B_bonded: 5.45 restraints_weight: 2.0000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2413 Z= 0.156 Angle : 0.538 5.939 3251 Z= 0.277 Chirality : 0.039 0.144 355 Planarity : 0.003 0.021 379 Dihedral : 10.916 88.350 479 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.46 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.52), residues: 266 helix: 3.13 (0.37), residues: 177 sheet: -0.38 (1.34), residues: 11 loop : -1.37 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 175 HIS 0.001 0.001 HIS C 396 PHE 0.011 0.001 PHE L 59 TYR 0.009 0.001 TYR C 421 ARG 0.003 0.000 ARG L 200 Details of bonding type rmsd hydrogen bonds : bond 0.04239 ( 156) hydrogen bonds : angle 3.93837 ( 452) SS BOND : bond 0.00598 ( 3) SS BOND : angle 1.18388 ( 6) covalent geometry : bond 0.00363 ( 2410) covalent geometry : angle 0.53634 ( 3245) *********************** 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: 4 poor density : 41 time to evaluate : 0.242 Fit side-chains REVERT: C 398 ARG cc_start: 0.6969 (mtp85) cc_final: 0.6641 (ptp-170) REVERT: C 401 LYS cc_start: 0.7311 (mtmm) cc_final: 0.6915 (mmmm) REVERT: H 698 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.7377 (m-10) REVERT: L 18 ASN cc_start: 0.7691 (m-40) cc_final: 0.7425 (m110) REVERT: L 200 ARG cc_start: 0.8294 (tpp80) cc_final: 0.7867 (ttt90) outliers start: 4 outliers final: 3 residues processed: 41 average time/residue: 0.9209 time to fit residues: 38.9746 Evaluate side-chains 44 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LEU 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 14 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3396 r_free = 0.3396 target = 0.101939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.070789 restraints weight = 13221.125| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 4.80 r_work: 0.2650 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 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 = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2826 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= 0.159 Angle : 0.541 6.014 3251 Z= 0.278 Chirality : 0.039 0.144 355 Planarity : 0.003 0.021 379 Dihedral : 10.745 87.078 479 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.61 % Allowed : 20.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.52), residues: 266 helix: 3.16 (0.37), residues: 177 sheet: -0.30 (1.32), residues: 11 loop : -1.36 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 175 HIS 0.001 0.001 HIS C 396 PHE 0.011 0.001 PHE L 59 TYR 0.009 0.001 TYR C 421 ARG 0.003 0.000 ARG L 200 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 156) hydrogen bonds : angle 3.94022 ( 452) SS BOND : bond 0.00590 ( 3) SS BOND : angle 1.09828 ( 6) covalent geometry : bond 0.00370 ( 2410) covalent geometry : angle 0.53928 ( 3245) *********************** 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 49 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.241 Fit side-chains REVERT: C 398 ARG cc_start: 0.6987 (mtp85) cc_final: 0.6479 (ptp-170) REVERT: C 401 LYS cc_start: 0.7308 (mtmm) cc_final: 0.6919 (mmmm) REVERT: H 698 TYR cc_start: 0.7837 (OUTLIER) cc_final: 0.7410 (m-10) REVERT: L 18 ASN cc_start: 0.7730 (m-40) cc_final: 0.7437 (m110) REVERT: L 200 ARG cc_start: 0.8280 (tpp80) cc_final: 0.7841 (ttt90) outliers start: 6 outliers final: 3 residues processed: 45 average time/residue: 0.8377 time to fit residues: 38.9469 Evaluate side-chains 44 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 0.0670 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 0.0060 chunk 19 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 overall best weight: 0.4334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.103145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.071918 restraints weight = 14774.130| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 5.01 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2837 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= 0.126 Angle : 0.521 6.128 3251 Z= 0.269 Chirality : 0.038 0.144 355 Planarity : 0.003 0.021 379 Dihedral : 10.358 84.705 479 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.52), residues: 266 helix: 3.24 (0.37), residues: 177 sheet: -0.17 (1.37), residues: 11 loop : -1.40 (0.68), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 175 HIS 0.001 0.000 HIS C 396 PHE 0.010 0.001 PHE L 59 TYR 0.008 0.001 TYR C 421 ARG 0.003 0.000 ARG L 200 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 156) hydrogen bonds : angle 3.90539 ( 452) SS BOND : bond 0.00482 ( 3) SS BOND : angle 0.95532 ( 6) covalent geometry : bond 0.00284 ( 2410) covalent geometry : angle 0.51941 ( 3245) ********************** 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 46 residues out of total 226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.267 Fit side-chains REVERT: C 398 ARG cc_start: 0.6871 (mtp85) cc_final: 0.6471 (ptp-170) REVERT: C 401 LYS cc_start: 0.7373 (mtmm) cc_final: 0.6892 (mmmm) REVERT: H 698 TYR cc_start: 0.7804 (m-80) cc_final: 0.7413 (m-10) REVERT: L 18 ASN cc_start: 0.7743 (m-40) cc_final: 0.7435 (m110) REVERT: L 200 ARG cc_start: 0.8159 (tpp80) cc_final: 0.7708 (ttt90) outliers start: 3 outliers final: 2 residues processed: 43 average time/residue: 0.8866 time to fit residues: 39.3335 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 : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 LEU 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 18 optimal weight: 0.0370 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 0.0010 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 0.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3424 r_free = 0.3424 target = 0.103876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.072583 restraints weight = 16795.944| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 5.27 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 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 0.027 2413 Z= 0.122 Angle : 0.523 6.162 3251 Z= 0.269 Chirality : 0.037 0.142 355 Planarity : 0.003 0.021 379 Dihedral : 10.142 83.874 479 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.67 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.52), residues: 266 helix: 3.21 (0.37), residues: 177 sheet: 0.11 (1.39), residues: 11 loop : -1.36 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 175 HIS 0.001 0.000 HIS C 396 PHE 0.013 0.001 PHE C 378 TYR 0.008 0.001 TYR C 421 ARG 0.003 0.000 ARG L 200 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 156) hydrogen bonds : angle 3.89047 ( 452) SS BOND : bond 0.00458 ( 3) SS BOND : angle 0.89243 ( 6) covalent geometry : bond 0.00273 ( 2410) covalent geometry : angle 0.52205 ( 3245) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2063.03 seconds wall clock time: 36 minutes 6.34 seconds (2166.34 seconds total)