Starting phenix.real_space_refine on Wed Jul 23 21:12:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dkw_27492/07_2025/8dkw_27492.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dkw_27492/07_2025/8dkw_27492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dkw_27492/07_2025/8dkw_27492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dkw_27492/07_2025/8dkw_27492.map" model { file = "/net/cci-nas-00/data/ceres_data/8dkw_27492/07_2025/8dkw_27492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dkw_27492/07_2025/8dkw_27492.cif" } resolution = 3.09 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= 0.004 sd= 0.082 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2863 2.51 5 N 704 2.21 5 O 788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4370 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 876 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "B" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2680 Classifications: {'peptide': 334} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 15, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 3.51, per 1000 atoms: 0.80 Number of scatterers: 4370 At special positions: 0 Unit cell: (78.85, 63.91, 122.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 788 8.00 N 704 7.00 C 2863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " 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: 1.08 Conformation dependent library (CDL) restraints added in 499.7 milliseconds 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 8 sheets defined 38.0% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.940A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.658A pdb=" N ASP A 91 " --> pdb=" O ARG A 88 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR A 92 " --> pdb=" O SER A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 92' Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.313A pdb=" N ILE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 139 removed outlier: 3.902A pdb=" N SER P 124 " --> pdb=" O SER P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 152 removed outlier: 3.891A pdb=" N GLN P 145 " --> pdb=" O SER P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 182 removed outlier: 3.629A pdb=" N THR P 168 " --> pdb=" O ALA P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 194 Processing helix chain 'P' and resid 202 through 226 removed outlier: 3.500A pdb=" N TYR P 226 " --> pdb=" O GLN P 222 " (cutoff:3.500A) Processing helix chain 'P' and resid 234 through 258 Processing helix chain 'P' and resid 263 through 290 removed outlier: 3.531A pdb=" N VAL P 276 " --> pdb=" O ILE P 272 " (cutoff:3.500A) Proline residue: P 283 - end of helix Processing helix chain 'P' and resid 298 through 323 removed outlier: 4.093A pdb=" N LEU P 303 " --> pdb=" O ILE P 299 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU P 313 " --> pdb=" O GLY P 309 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN P 323 " --> pdb=" O GLN P 319 " (cutoff:3.500A) Processing helix chain 'P' and resid 334 through 356 removed outlier: 3.567A pdb=" N LEU P 338 " --> pdb=" O THR P 334 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.604A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 6 removed outlier: 12.172A pdb=" N CYS B 23 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 11.336A pdb=" N ALA B 74 " --> pdb=" O CYS B 23 " (cutoff:3.500A) removed outlier: 11.467A pdb=" N ALA B 25 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 11.318A pdb=" N THR B 72 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N GLN B 27 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASP B 70 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.436A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 44 through 48 removed outlier: 6.356A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 26 through 27 Processing sheet with id=AA7, first strand: chain 'P' and resid 31 through 35 removed outlier: 6.934A pdb=" N VAL P 32 " --> pdb=" O LEU P 116 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE P 118 " --> pdb=" O VAL P 32 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU P 34 " --> pdb=" O ILE P 118 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR P 98 " --> pdb=" O THR P 61 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 39 through 43 removed outlier: 3.596A pdb=" N THR P 90 " --> pdb=" O GLU P 71 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 597 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: 1.09 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1336 1.34 - 1.46: 932 1.46 - 1.57: 2200 1.57 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 4490 Sorted by residual: bond pdb=" N ILE P 260 " pdb=" CA ILE P 260 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.00e+00 bond pdb=" N VAL P 259 " pdb=" CA VAL P 259 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.41e-02 5.03e+03 7.52e+00 bond pdb=" N TRP P 262 " pdb=" CA TRP P 262 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.37e-02 5.33e+03 6.84e+00 bond pdb=" N THR P 261 " pdb=" CA THR P 261 " ideal model delta sigma weight residual 1.460 1.500 -0.040 1.83e-02 2.99e+03 4.73e+00 bond pdb=" N GLY P 258 " pdb=" CA GLY P 258 " ideal model delta sigma weight residual 1.449 1.480 -0.031 1.45e-02 4.76e+03 4.53e+00 ... (remaining 4485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 5868 1.54 - 3.08: 203 3.08 - 4.63: 39 4.63 - 6.17: 10 6.17 - 7.71: 2 Bond angle restraints: 6122 Sorted by residual: angle pdb=" CA ILE P 260 " pdb=" C ILE P 260 " pdb=" O ILE P 260 " ideal model delta sigma weight residual 120.95 116.30 4.65 1.04e+00 9.25e-01 2.00e+01 angle pdb=" C THR P 261 " pdb=" CA THR P 261 " pdb=" CB THR P 261 " ideal model delta sigma weight residual 110.04 115.18 -5.14 1.51e+00 4.39e-01 1.16e+01 angle pdb=" C PRO P 195 " pdb=" N ASN P 196 " pdb=" CA ASN P 196 " ideal model delta sigma weight residual 121.54 127.50 -5.96 1.91e+00 2.74e-01 9.73e+00 angle pdb=" C ILE P 133 " pdb=" N TYR P 134 " pdb=" CA TYR P 134 " ideal model delta sigma weight residual 121.14 115.90 5.24 1.75e+00 3.27e-01 8.96e+00 angle pdb=" C ILE P 260 " pdb=" CA ILE P 260 " pdb=" CB ILE P 260 " ideal model delta sigma weight residual 112.14 115.64 -3.50 1.35e+00 5.49e-01 6.74e+00 ... (remaining 6117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 2316 17.84 - 35.68: 230 35.68 - 53.52: 32 53.52 - 71.36: 2 71.36 - 89.20: 3 Dihedral angle restraints: 2583 sinusoidal: 986 harmonic: 1597 Sorted by residual: dihedral pdb=" C THR P 261 " pdb=" N THR P 261 " pdb=" CA THR P 261 " pdb=" CB THR P 261 " ideal model delta harmonic sigma weight residual -122.00 -142.14 20.14 0 2.50e+00 1.60e-01 6.49e+01 dihedral pdb=" N THR P 261 " pdb=" C THR P 261 " pdb=" CA THR P 261 " pdb=" CB THR P 261 " ideal model delta harmonic sigma weight residual 123.40 142.24 -18.84 0 2.50e+00 1.60e-01 5.68e+01 dihedral pdb=" CA ARG P 112 " pdb=" C ARG P 112 " pdb=" N ILE P 113 " pdb=" CA ILE P 113 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 2580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 688 0.161 - 0.321: 4 0.321 - 0.482: 0 0.482 - 0.642: 0 0.642 - 0.803: 1 Chirality restraints: 693 Sorted by residual: chirality pdb=" CA THR P 261 " pdb=" N THR P 261 " pdb=" C THR P 261 " pdb=" CB THR P 261 " both_signs ideal model delta sigma weight residual False 2.53 1.72 0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CB THR P 261 " pdb=" CA THR P 261 " pdb=" OG1 THR P 261 " pdb=" CG2 THR P 261 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB VAL P 259 " pdb=" CA VAL P 259 " pdb=" CG1 VAL P 259 " pdb=" CG2 VAL P 259 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 690 not shown) Planarity restraints: 764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP P 235 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO P 236 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO P 236 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO P 236 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG P 47 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO P 48 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO P 48 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO P 48 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 269 " 0.007 2.00e-02 2.50e+03 9.62e-03 1.62e+00 pdb=" CG PHE P 269 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE P 269 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE P 269 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE P 269 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE P 269 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE P 269 " -0.001 2.00e-02 2.50e+03 ... (remaining 761 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 77 2.66 - 3.22: 4170 3.22 - 3.78: 6492 3.78 - 4.34: 9068 4.34 - 4.90: 15515 Nonbonded interactions: 35322 Sorted by model distance: nonbonded pdb=" OH TYR P 134 " pdb=" OD1 ASP P 205 " model vdw 2.097 3.040 nonbonded pdb=" OE1 GLN B 6 " pdb=" OG1 THR B 102 " model vdw 2.169 3.040 nonbonded pdb=" NH2 ARG A 68 " pdb=" OD2 ASP A 91 " model vdw 2.181 3.120 nonbonded pdb=" OG1 THR A 40 " pdb=" O GLU A 42 " model vdw 2.183 3.040 nonbonded pdb=" OG1 THR A 28 " pdb=" OD1 ASN A 31 " model vdw 2.234 3.040 ... (remaining 35317 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.940 Find NCS groups from input model: 0.070 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 0.006 0.045 4492 Z= 0.260 Angle : 0.711 7.709 6126 Z= 0.405 Chirality : 0.058 0.803 693 Planarity : 0.004 0.043 764 Dihedral : 13.839 89.198 1557 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.41 % Allowed : 7.47 % Favored : 92.12 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 4.17 % 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: -2.92 (0.31), residues: 547 helix: -0.87 (0.31), residues: 199 sheet: -2.01 (0.38), residues: 149 loop : -2.84 (0.38), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 132 HIS 0.007 0.001 HIS B 55 PHE 0.022 0.001 PHE P 269 TYR 0.013 0.001 TYR A 100 ARG 0.006 0.001 ARG P 112 Details of bonding type rmsd hydrogen bonds : bond 0.11747 ( 211) hydrogen bonds : angle 6.76519 ( 597) SS BOND : bond 0.00214 ( 2) SS BOND : angle 0.32373 ( 4) covalent geometry : bond 0.00592 ( 4490) covalent geometry : angle 0.71100 ( 6122) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.461 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8201 (tttp) cc_final: 0.7871 (tttm) REVERT: B 79 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8218 (mt0) REVERT: P 140 ILE cc_start: 0.7610 (tt) cc_final: 0.7170 (tp) REVERT: P 223 CYS cc_start: 0.7044 (p) cc_final: 0.6765 (p) outliers start: 2 outliers final: 0 residues processed: 63 average time/residue: 0.1694 time to fit residues: 13.6260 Evaluate side-chains 56 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.0040 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN B 6 GLN B 28 ASN B 38 GLN P 222 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.169140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.129486 restraints weight = 4848.135| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.32 r_work: 0.3417 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4492 Z= 0.134 Angle : 0.573 6.548 6126 Z= 0.300 Chirality : 0.045 0.177 693 Planarity : 0.004 0.037 764 Dihedral : 4.888 18.739 596 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.87 % Allowed : 13.07 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.51 (0.34), residues: 547 helix: 0.86 (0.35), residues: 197 sheet: -1.53 (0.42), residues: 136 loop : -2.41 (0.36), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 262 HIS 0.002 0.001 HIS B 55 PHE 0.017 0.001 PHE P 269 TYR 0.014 0.001 TYR P 134 ARG 0.005 0.001 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 211) hydrogen bonds : angle 4.99633 ( 597) SS BOND : bond 0.00358 ( 2) SS BOND : angle 0.45532 ( 4) covalent geometry : bond 0.00304 ( 4490) covalent geometry : angle 0.57272 ( 6122) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.461 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8184 (tttp) cc_final: 0.7759 (tttm) REVERT: B 79 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8082 (mt0) REVERT: P 71 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8115 (mt-10) REVERT: P 140 ILE cc_start: 0.7752 (tt) cc_final: 0.7122 (tp) REVERT: P 148 MET cc_start: 0.7733 (tmm) cc_final: 0.7506 (tmm) REVERT: P 269 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.7023 (m-80) REVERT: P 332 ASP cc_start: 0.8481 (t0) cc_final: 0.8243 (t0) outliers start: 9 outliers final: 4 residues processed: 61 average time/residue: 0.1837 time to fit residues: 14.5475 Evaluate side-chains 59 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.6980 chunk 10 optimal weight: 0.0770 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.171388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133018 restraints weight = 4824.850| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.25 r_work: 0.3408 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4492 Z= 0.152 Angle : 0.561 6.609 6126 Z= 0.291 Chirality : 0.045 0.162 693 Planarity : 0.004 0.033 764 Dihedral : 4.829 17.972 596 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.49 % Allowed : 14.94 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.00 (0.35), residues: 547 helix: 1.35 (0.36), residues: 197 sheet: -1.26 (0.43), residues: 136 loop : -2.20 (0.36), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 132 HIS 0.002 0.001 HIS B 55 PHE 0.015 0.001 PHE P 269 TYR 0.015 0.001 TYR P 134 ARG 0.004 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 211) hydrogen bonds : angle 4.75650 ( 597) SS BOND : bond 0.00195 ( 2) SS BOND : angle 0.36108 ( 4) covalent geometry : bond 0.00361 ( 4490) covalent geometry : angle 0.56127 ( 6122) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.435 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8149 (tttp) cc_final: 0.7799 (tttm) REVERT: A 85 SER cc_start: 0.8413 (p) cc_final: 0.8087 (m) REVERT: P 71 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8167 (mt-10) REVERT: P 140 ILE cc_start: 0.7727 (tt) cc_final: 0.7089 (tp) REVERT: P 148 MET cc_start: 0.7785 (tmm) cc_final: 0.7427 (tmm) REVERT: P 269 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.7019 (m-80) outliers start: 12 outliers final: 8 residues processed: 63 average time/residue: 0.1786 time to fit residues: 14.3223 Evaluate side-chains 62 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.171150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.131130 restraints weight = 4925.424| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.38 r_work: 0.3390 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4492 Z= 0.157 Angle : 0.556 6.392 6126 Z= 0.288 Chirality : 0.045 0.148 693 Planarity : 0.004 0.032 764 Dihedral : 4.780 17.656 596 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.70 % Allowed : 16.60 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.83 (0.35), residues: 547 helix: 1.33 (0.36), residues: 203 sheet: -1.20 (0.44), residues: 136 loop : -1.99 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 235 HIS 0.002 0.001 HIS B 55 PHE 0.015 0.001 PHE P 269 TYR 0.014 0.001 TYR P 134 ARG 0.005 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 211) hydrogen bonds : angle 4.65635 ( 597) SS BOND : bond 0.00246 ( 2) SS BOND : angle 0.49678 ( 4) covalent geometry : bond 0.00378 ( 4490) covalent geometry : angle 0.55599 ( 6122) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.469 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8145 (tttp) cc_final: 0.7799 (tttm) REVERT: A 85 SER cc_start: 0.8460 (p) cc_final: 0.8122 (m) REVERT: B 4 MET cc_start: 0.8212 (mmm) cc_final: 0.7939 (mmm) REVERT: B 61 ARG cc_start: 0.7731 (mtp180) cc_final: 0.7195 (ptm160) REVERT: B 82 ASP cc_start: 0.8365 (m-30) cc_final: 0.7670 (m-30) REVERT: P 148 MET cc_start: 0.7801 (tmm) cc_final: 0.7418 (tmm) REVERT: P 269 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.7079 (m-80) outliers start: 13 outliers final: 8 residues processed: 62 average time/residue: 0.1551 time to fit residues: 12.5510 Evaluate side-chains 60 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Chi-restraints excluded: chain P residue 330 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 0.0050 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.169741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.129861 restraints weight = 5046.645| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.40 r_work: 0.3409 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4492 Z= 0.136 Angle : 0.531 6.073 6126 Z= 0.275 Chirality : 0.044 0.149 693 Planarity : 0.003 0.032 764 Dihedral : 4.655 16.693 596 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.90 % Allowed : 17.01 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.62 (0.36), residues: 547 helix: 1.51 (0.36), residues: 203 sheet: -1.12 (0.44), residues: 141 loop : -1.85 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 132 HIS 0.001 0.000 HIS B 55 PHE 0.016 0.001 PHE P 269 TYR 0.014 0.001 TYR P 134 ARG 0.005 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 211) hydrogen bonds : angle 4.54092 ( 597) SS BOND : bond 0.00144 ( 2) SS BOND : angle 0.34263 ( 4) covalent geometry : bond 0.00321 ( 4490) covalent geometry : angle 0.53075 ( 6122) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.432 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8144 (tttp) cc_final: 0.7799 (tttm) REVERT: A 55 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7374 (pm20) REVERT: A 85 SER cc_start: 0.8435 (p) cc_final: 0.8104 (m) REVERT: B 61 ARG cc_start: 0.7745 (mtp180) cc_final: 0.7226 (ptm160) REVERT: B 82 ASP cc_start: 0.8296 (m-30) cc_final: 0.7758 (m-30) REVERT: P 148 MET cc_start: 0.7799 (tmm) cc_final: 0.7419 (tmm) REVERT: P 180 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7911 (mp) REVERT: P 189 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: P 269 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.7081 (m-80) outliers start: 14 outliers final: 7 residues processed: 66 average time/residue: 0.1515 time to fit residues: 13.1535 Evaluate side-chains 63 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 189 GLN Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 0.0570 chunk 6 optimal weight: 0.0060 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.173962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.135058 restraints weight = 4921.459| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.33 r_work: 0.3463 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4492 Z= 0.126 Angle : 0.527 5.849 6126 Z= 0.272 Chirality : 0.044 0.143 693 Planarity : 0.003 0.035 764 Dihedral : 4.566 16.738 596 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.70 % Allowed : 18.67 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.51 (0.36), residues: 547 helix: 1.56 (0.36), residues: 205 sheet: -1.07 (0.44), residues: 141 loop : -1.75 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 132 HIS 0.001 0.000 HIS B 55 PHE 0.016 0.001 PHE P 269 TYR 0.013 0.001 TYR P 134 ARG 0.002 0.000 ARG A 73 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 211) hydrogen bonds : angle 4.45057 ( 597) SS BOND : bond 0.00230 ( 2) SS BOND : angle 0.52026 ( 4) covalent geometry : bond 0.00294 ( 4490) covalent geometry : angle 0.52682 ( 6122) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.420 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8077 (tttp) cc_final: 0.7721 (tttm) REVERT: A 55 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7333 (pm20) REVERT: A 85 SER cc_start: 0.8446 (p) cc_final: 0.8089 (m) REVERT: B 4 MET cc_start: 0.8150 (mmm) cc_final: 0.7825 (mmm) REVERT: B 61 ARG cc_start: 0.7639 (mtp180) cc_final: 0.7067 (ptm160) REVERT: B 82 ASP cc_start: 0.8240 (m-30) cc_final: 0.7659 (m-30) REVERT: P 67 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7134 (tp) REVERT: P 74 ASP cc_start: 0.8657 (t70) cc_final: 0.8325 (t0) REVERT: P 148 MET cc_start: 0.7702 (tmm) cc_final: 0.7308 (tmm) REVERT: P 180 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7784 (mp) REVERT: P 189 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: P 269 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.6963 (m-80) outliers start: 13 outliers final: 7 residues processed: 65 average time/residue: 0.1459 time to fit residues: 12.4561 Evaluate side-chains 66 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 189 GLN Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.166226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126398 restraints weight = 4946.250| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.34 r_work: 0.3371 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4492 Z= 0.201 Angle : 0.580 6.421 6126 Z= 0.300 Chirality : 0.046 0.152 693 Planarity : 0.004 0.034 764 Dihedral : 4.810 17.265 596 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.73 % Allowed : 18.88 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.74 (0.36), residues: 547 helix: 1.39 (0.36), residues: 205 sheet: -1.28 (0.41), residues: 150 loop : -1.83 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 132 HIS 0.002 0.001 HIS B 55 PHE 0.016 0.001 PHE P 269 TYR 0.018 0.001 TYR P 134 ARG 0.003 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04033 ( 211) hydrogen bonds : angle 4.64491 ( 597) SS BOND : bond 0.00131 ( 2) SS BOND : angle 0.57475 ( 4) covalent geometry : bond 0.00492 ( 4490) covalent geometry : angle 0.57991 ( 6122) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.463 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8129 (tttp) cc_final: 0.7721 (tttm) REVERT: A 31 ASN cc_start: 0.8575 (m-40) cc_final: 0.8302 (m110) REVERT: A 55 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: B 61 ARG cc_start: 0.7804 (mtp180) cc_final: 0.7100 (ptm160) REVERT: B 82 ASP cc_start: 0.8304 (m-30) cc_final: 0.7690 (m-30) REVERT: P 67 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7125 (tp) REVERT: P 148 MET cc_start: 0.7769 (tmm) cc_final: 0.7386 (tmm) REVERT: P 180 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.7922 (mp) REVERT: P 189 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: P 269 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7104 (m-80) outliers start: 18 outliers final: 8 residues processed: 67 average time/residue: 0.1480 time to fit residues: 13.0461 Evaluate side-chains 64 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 189 GLN Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Chi-restraints excluded: chain P residue 330 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 0.0060 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.0170 chunk 42 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 overall best weight: 0.2234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN B 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.174863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135530 restraints weight = 4887.960| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.39 r_work: 0.3482 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4492 Z= 0.096 Angle : 0.494 5.394 6126 Z= 0.258 Chirality : 0.043 0.140 693 Planarity : 0.003 0.036 764 Dihedral : 4.419 16.286 596 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.28 % Allowed : 21.37 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.29 (0.36), residues: 547 helix: 1.78 (0.36), residues: 205 sheet: -1.08 (0.44), residues: 142 loop : -1.57 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 32 HIS 0.001 0.000 HIS B 55 PHE 0.018 0.001 PHE P 269 TYR 0.010 0.001 TYR P 134 ARG 0.002 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.02981 ( 211) hydrogen bonds : angle 4.28735 ( 597) SS BOND : bond 0.00335 ( 2) SS BOND : angle 0.64166 ( 4) covalent geometry : bond 0.00206 ( 4490) covalent geometry : angle 0.49343 ( 6122) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.434 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8100 (tttp) cc_final: 0.7770 (tttm) REVERT: A 85 SER cc_start: 0.8430 (OUTLIER) cc_final: 0.8086 (m) REVERT: B 61 ARG cc_start: 0.7689 (mtp180) cc_final: 0.7189 (ptm160) REVERT: B 82 ASP cc_start: 0.8155 (m-30) cc_final: 0.7730 (m-30) REVERT: P 67 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.6993 (tp) REVERT: P 74 ASP cc_start: 0.8589 (t70) cc_final: 0.8297 (t0) REVERT: P 148 MET cc_start: 0.7853 (tmm) cc_final: 0.7435 (tmm) REVERT: P 180 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7755 (mp) REVERT: P 189 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: P 269 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.7096 (m-80) outliers start: 11 outliers final: 5 residues processed: 64 average time/residue: 0.1537 time to fit residues: 12.9540 Evaluate side-chains 62 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 189 GLN Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.0970 chunk 1 optimal weight: 5.9990 chunk 38 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.176605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.137601 restraints weight = 4993.146| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.39 r_work: 0.3469 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4492 Z= 0.107 Angle : 0.501 5.476 6126 Z= 0.260 Chirality : 0.043 0.141 693 Planarity : 0.003 0.034 764 Dihedral : 4.405 16.186 596 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.28 % Allowed : 21.78 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.17 (0.37), residues: 547 helix: 1.88 (0.36), residues: 205 sheet: -1.03 (0.44), residues: 142 loop : -1.50 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 132 HIS 0.001 0.000 HIS B 55 PHE 0.016 0.001 PHE P 269 TYR 0.012 0.001 TYR P 134 ARG 0.003 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 211) hydrogen bonds : angle 4.28415 ( 597) SS BOND : bond 0.00324 ( 2) SS BOND : angle 0.99298 ( 4) covalent geometry : bond 0.00245 ( 4490) covalent geometry : angle 0.50004 ( 6122) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.467 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 66 ARG cc_start: 0.8588 (tpp80) cc_final: 0.7991 (ttp-170) REVERT: A 85 SER cc_start: 0.8502 (OUTLIER) cc_final: 0.8157 (m) REVERT: B 61 ARG cc_start: 0.7757 (mtp180) cc_final: 0.7401 (ptp-170) REVERT: P 67 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.6863 (tp) REVERT: P 74 ASP cc_start: 0.8502 (t70) cc_final: 0.8257 (t0) REVERT: P 148 MET cc_start: 0.7807 (tmm) cc_final: 0.7423 (tmm) REVERT: P 180 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7792 (mp) REVERT: P 189 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: P 269 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.6867 (m-80) outliers start: 11 outliers final: 6 residues processed: 60 average time/residue: 0.1390 time to fit residues: 11.1960 Evaluate side-chains 61 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 189 GLN Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.171953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.132612 restraints weight = 4876.791| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.35 r_work: 0.3414 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4492 Z= 0.164 Angle : 0.547 6.131 6126 Z= 0.283 Chirality : 0.045 0.148 693 Planarity : 0.003 0.034 764 Dihedral : 4.633 16.958 596 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.70 % Allowed : 21.58 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.28 (0.36), residues: 547 helix: 1.75 (0.36), residues: 205 sheet: -1.08 (0.44), residues: 142 loop : -1.52 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 132 HIS 0.001 0.000 HIS B 55 PHE 0.015 0.001 PHE P 269 TYR 0.017 0.001 TYR P 134 ARG 0.004 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 211) hydrogen bonds : angle 4.45475 ( 597) SS BOND : bond 0.00300 ( 2) SS BOND : angle 1.38485 ( 4) covalent geometry : bond 0.00396 ( 4490) covalent geometry : angle 0.54645 ( 6122) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.484 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8093 (tttp) cc_final: 0.7747 (tttm) REVERT: A 85 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.8141 (m) REVERT: P 67 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.6919 (tp) REVERT: P 145 GLN cc_start: 0.7438 (tp40) cc_final: 0.7236 (tp40) REVERT: P 148 MET cc_start: 0.7767 (tmm) cc_final: 0.7349 (tmm) REVERT: P 180 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.7863 (mp) REVERT: P 189 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8281 (tt0) REVERT: P 269 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.7073 (m-80) outliers start: 13 outliers final: 7 residues processed: 62 average time/residue: 0.2196 time to fit residues: 17.5617 Evaluate side-chains 64 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 189 GLN Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 277 THR Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.173133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.134035 restraints weight = 4951.959| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.34 r_work: 0.3425 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4492 Z= 0.142 Angle : 0.531 6.081 6126 Z= 0.275 Chirality : 0.044 0.147 693 Planarity : 0.003 0.035 764 Dihedral : 4.603 16.616 596 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.90 % Allowed : 21.37 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.25 (0.36), residues: 547 helix: 1.78 (0.36), residues: 205 sheet: -1.09 (0.44), residues: 142 loop : -1.47 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 235 HIS 0.001 0.000 HIS B 55 PHE 0.015 0.001 PHE P 269 TYR 0.015 0.001 TYR P 134 ARG 0.004 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 211) hydrogen bonds : angle 4.41337 ( 597) SS BOND : bond 0.00269 ( 2) SS BOND : angle 1.25750 ( 4) covalent geometry : bond 0.00340 ( 4490) covalent geometry : angle 0.53064 ( 6122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2935.21 seconds wall clock time: 51 minutes 49.70 seconds (3109.70 seconds total)