Starting phenix.real_space_refine on Wed Mar 5 15:18:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l4s_0833/03_2025/6l4s_0833.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l4s_0833/03_2025/6l4s_0833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6l4s_0833/03_2025/6l4s_0833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l4s_0833/03_2025/6l4s_0833.map" model { file = "/net/cci-nas-00/data/ceres_data/6l4s_0833/03_2025/6l4s_0833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l4s_0833/03_2025/6l4s_0833.cif" } resolution = 3.37 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= 0.001 sd= 0.008 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: 3 Type Number sf(0) Gaussians C 1410 2.51 5 N 408 2.21 5 O 450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2268 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 1.20, per 1000 atoms: 0.53 Number of scatterers: 2268 At special positions: 0 Unit cell: (83.79, 91.77, 35.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 450 8.00 N 408 7.00 C 1410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.50 Conformation dependent library (CDL) restraints added in 408.8 milliseconds 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 48 removed outlier: 6.361A pdb=" N GLY A 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 63 through 64 removed outlier: 6.156A pdb=" N GLU A 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N THR E 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL A 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 69 through 71 removed outlier: 6.585A pdb=" N VAL A 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 75 through 78 removed outlier: 6.275A pdb=" N ALA A 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 93 removed outlier: 6.831A pdb=" N THR C 92 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N THR A 92 " --> pdb=" O GLY E 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 46 through 48 removed outlier: 6.552A pdb=" N GLY B 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 63 through 64 removed outlier: 6.327A pdb=" N VAL B 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.438A pdb=" N VAL B 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 75 through 78 removed outlier: 6.474A pdb=" N THR B 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ALA D 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL B 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 91 through 93 removed outlier: 6.880A pdb=" N THR D 92 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N THR B 92 " --> pdb=" O GLY F 93 " (cutoff:3.500A) 19 hydrogen bonds defined for protein. 54 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: 0.42 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 402 1.28 - 1.35: 360 1.35 - 1.42: 60 1.42 - 1.49: 538 1.49 - 1.56: 914 Bond restraints: 2274 Sorted by residual: bond pdb=" CB VAL E 74 " pdb=" CG1 VAL E 74 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.51e+00 bond pdb=" CB VAL D 74 " pdb=" CG1 VAL D 74 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.51e+00 bond pdb=" CB VAL A 74 " pdb=" CG1 VAL A 74 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.46e+00 bond pdb=" CB VAL F 74 " pdb=" CG1 VAL F 74 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.45e+00 bond pdb=" CB VAL C 74 " pdb=" CG1 VAL C 74 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.45e+00 ... (remaining 2269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 2626 1.67 - 3.34: 326 3.34 - 5.01: 96 5.01 - 6.68: 12 6.68 - 8.35: 6 Bond angle restraints: 3066 Sorted by residual: angle pdb=" C VAL C 66 " pdb=" N GLY C 67 " pdb=" CA GLY C 67 " ideal model delta sigma weight residual 121.41 113.06 8.35 1.96e+00 2.60e-01 1.81e+01 angle pdb=" C VAL F 66 " pdb=" N GLY F 67 " pdb=" CA GLY F 67 " ideal model delta sigma weight residual 121.41 113.08 8.33 1.96e+00 2.60e-01 1.81e+01 angle pdb=" C VAL D 66 " pdb=" N GLY D 67 " pdb=" CA GLY D 67 " ideal model delta sigma weight residual 121.41 113.10 8.31 1.96e+00 2.60e-01 1.80e+01 angle pdb=" C VAL A 66 " pdb=" N GLY A 67 " pdb=" CA GLY A 67 " ideal model delta sigma weight residual 121.41 113.11 8.30 1.96e+00 2.60e-01 1.79e+01 angle pdb=" C VAL B 66 " pdb=" N GLY B 67 " pdb=" CA GLY B 67 " ideal model delta sigma weight residual 121.41 113.12 8.29 1.96e+00 2.60e-01 1.79e+01 ... (remaining 3061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.36: 1020 7.36 - 14.71: 222 14.71 - 22.07: 78 22.07 - 29.42: 12 29.42 - 36.78: 12 Dihedral angle restraints: 1344 sinusoidal: 456 harmonic: 888 Sorted by residual: dihedral pdb=" CA GLY C 93 " pdb=" C GLY C 93 " pdb=" N PHE C 94 " pdb=" CA PHE C 94 " ideal model delta harmonic sigma weight residual -180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLY E 93 " pdb=" C GLY E 93 " pdb=" N PHE E 94 " pdb=" CA PHE E 94 " ideal model delta harmonic sigma weight residual -180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLY D 93 " pdb=" C GLY D 93 " pdb=" N PHE D 94 " pdb=" CA PHE D 94 " ideal model delta harmonic sigma weight residual 180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 1341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 289 0.087 - 0.175: 101 0.175 - 0.262: 6 0.262 - 0.349: 0 0.349 - 0.436: 6 Chirality restraints: 402 Sorted by residual: chirality pdb=" CB VAL E 95 " pdb=" CA VAL E 95 " pdb=" CG1 VAL E 95 " pdb=" CG2 VAL E 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" CB VAL F 95 " pdb=" CA VAL F 95 " pdb=" CG1 VAL F 95 " pdb=" CG2 VAL F 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" CB VAL D 95 " pdb=" CA VAL D 95 " pdb=" CG1 VAL D 95 " pdb=" CG2 VAL D 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.74e+00 ... (remaining 399 not shown) Planarity restraints: 384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 52 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.13e+00 pdb=" C VAL C 52 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL C 52 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA C 53 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 52 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C VAL B 52 " 0.039 2.00e-02 2.50e+03 pdb=" O VAL B 52 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA B 53 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 52 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C VAL A 52 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL A 52 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA A 53 " 0.013 2.00e-02 2.50e+03 ... (remaining 381 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 961 2.91 - 3.40: 1874 3.40 - 3.90: 3350 3.90 - 4.40: 3778 4.40 - 4.90: 7475 Nonbonded interactions: 17438 Sorted by model distance: nonbonded pdb=" OG1 THR A 54 " pdb=" OG1 THR E 64 " model vdw 2.408 3.040 nonbonded pdb=" OG1 THR B 54 " pdb=" OG1 THR F 64 " model vdw 2.459 3.040 nonbonded pdb=" OG1 THR B 64 " pdb=" OG1 THR D 54 " model vdw 2.510 3.040 nonbonded pdb=" OD1 ASP A 98 " pdb=" N GLN A 99 " model vdw 2.524 3.120 nonbonded pdb=" OD1 ASP F 98 " pdb=" N GLN F 99 " model vdw 2.524 3.120 ... (remaining 17433 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 0.210 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.530 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 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 : 0.014 0.070 2274 Z= 0.956 Angle : 1.363 8.347 3066 Z= 0.791 Chirality : 0.091 0.436 402 Planarity : 0.006 0.023 384 Dihedral : 10.279 36.779 780 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.73 (0.35), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.27), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.015 0.007 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.240 Fit side-chains REVERT: A 57 GLU cc_start: 0.7206 (tt0) cc_final: 0.6883 (tm-30) REVERT: A 58 LYS cc_start: 0.7161 (mmtp) cc_final: 0.6738 (tptm) REVERT: A 62 GLN cc_start: 0.8097 (mt0) cc_final: 0.7745 (mt0) REVERT: A 83 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7756 (mp0) REVERT: A 97 LYS cc_start: 0.7233 (mmtt) cc_final: 0.7028 (mmtm) REVERT: B 57 GLU cc_start: 0.7007 (tt0) cc_final: 0.6717 (tm-30) REVERT: B 58 LYS cc_start: 0.7282 (mmtp) cc_final: 0.6721 (mmtt) REVERT: B 62 GLN cc_start: 0.7760 (mt0) cc_final: 0.7266 (mt0) REVERT: B 64 THR cc_start: 0.7588 (m) cc_final: 0.7323 (m) REVERT: B 97 LYS cc_start: 0.7663 (mmtt) cc_final: 0.7125 (mmtt) REVERT: C 57 GLU cc_start: 0.7398 (tt0) cc_final: 0.7084 (tm-30) REVERT: C 58 LYS cc_start: 0.8372 (mmtp) cc_final: 0.8151 (mmtt) REVERT: C 97 LYS cc_start: 0.8343 (mmtt) cc_final: 0.6588 (mtmt) REVERT: D 57 GLU cc_start: 0.7498 (tt0) cc_final: 0.6755 (tm-30) REVERT: D 58 LYS cc_start: 0.8257 (mmtp) cc_final: 0.7518 (mmmt) REVERT: D 62 GLN cc_start: 0.7601 (mt0) cc_final: 0.7329 (mt0) REVERT: D 97 LYS cc_start: 0.8331 (mmtt) cc_final: 0.7916 (mmtt) REVERT: E 57 GLU cc_start: 0.8203 (tt0) cc_final: 0.7890 (tm-30) REVERT: E 58 LYS cc_start: 0.7863 (mmtp) cc_final: 0.7503 (mmtt) REVERT: E 83 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7575 (pm20) REVERT: F 57 GLU cc_start: 0.7886 (tt0) cc_final: 0.7412 (tm-30) REVERT: F 58 LYS cc_start: 0.7217 (mmtp) cc_final: 0.6507 (mmmt) REVERT: F 97 LYS cc_start: 0.6886 (mmtt) cc_final: 0.6606 (mmtm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2296 time to fit residues: 19.4889 Evaluate side-chains 77 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4576 r_free = 0.4576 target = 0.175998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.133210 restraints weight = 2481.037| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 3.92 r_work: 0.4065 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2274 Z= 0.263 Angle : 0.614 4.492 3066 Z= 0.340 Chirality : 0.052 0.156 402 Planarity : 0.002 0.015 384 Dihedral : 6.341 17.530 324 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.51 % Allowed : 19.74 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.40 (0.36), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.28), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.009 0.002 PHE B 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.248 Fit side-chains REVERT: A 57 GLU cc_start: 0.8033 (tt0) cc_final: 0.7587 (tm-30) REVERT: A 58 LYS cc_start: 0.7859 (mmtp) cc_final: 0.7255 (tptm) REVERT: A 60 LYS cc_start: 0.8557 (mptt) cc_final: 0.8302 (mmtp) REVERT: B 57 GLU cc_start: 0.7753 (tt0) cc_final: 0.7182 (tm-30) REVERT: B 58 LYS cc_start: 0.7967 (mmtp) cc_final: 0.7622 (mttt) REVERT: B 97 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7704 (mmtt) REVERT: C 57 GLU cc_start: 0.7863 (tt0) cc_final: 0.7540 (tm-30) REVERT: D 57 GLU cc_start: 0.8000 (tt0) cc_final: 0.7569 (tm-30) REVERT: E 55 VAL cc_start: 0.8677 (t) cc_final: 0.8466 (t) REVERT: E 60 LYS cc_start: 0.8710 (tptt) cc_final: 0.8446 (mptt) REVERT: F 45 LYS cc_start: 0.5402 (mmtt) cc_final: 0.5093 (mmtm) REVERT: F 57 GLU cc_start: 0.8257 (tt0) cc_final: 0.7659 (tm-30) REVERT: F 58 LYS cc_start: 0.8050 (mmtp) cc_final: 0.7053 (mmmt) REVERT: F 59 THR cc_start: 0.8650 (m) cc_final: 0.8293 (t) REVERT: F 62 GLN cc_start: 0.7544 (mt0) cc_final: 0.7072 (mt0) REVERT: F 97 LYS cc_start: 0.7986 (mmtt) cc_final: 0.7504 (mmtm) outliers start: 8 outliers final: 8 residues processed: 75 average time/residue: 0.2208 time to fit residues: 18.3461 Evaluate side-chains 71 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 0.0570 chunk 15 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.0300 ------------------------------------------------------------------------------- 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 = 0.4770 r_free = 0.4770 target = 0.191554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.148324 restraints weight = 2347.739| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 3.89 r_work: 0.4254 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2274 Z= 0.133 Angle : 0.490 4.020 3066 Z= 0.270 Chirality : 0.051 0.144 402 Planarity : 0.002 0.012 384 Dihedral : 5.188 15.167 324 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.75 % Allowed : 26.32 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.13 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.006 0.001 PHE F 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.248 Fit side-chains REVERT: A 57 GLU cc_start: 0.8055 (tt0) cc_final: 0.7758 (tm-30) REVERT: A 58 LYS cc_start: 0.8215 (mmtp) cc_final: 0.7995 (tptt) REVERT: A 60 LYS cc_start: 0.8563 (mptt) cc_final: 0.8094 (mmtp) REVERT: B 58 LYS cc_start: 0.8018 (mmtp) cc_final: 0.7500 (mmmm) REVERT: C 58 LYS cc_start: 0.8488 (mmtt) cc_final: 0.8112 (mmtt) REVERT: C 97 LYS cc_start: 0.8065 (mmtp) cc_final: 0.5118 (ptpt) REVERT: D 57 GLU cc_start: 0.7944 (tt0) cc_final: 0.7643 (tm-30) REVERT: D 96 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7560 (mttt) REVERT: D 97 LYS cc_start: 0.7979 (mmtp) cc_final: 0.4863 (ptpt) REVERT: F 45 LYS cc_start: 0.5095 (mmtt) cc_final: 0.4894 (mmtm) REVERT: F 62 GLN cc_start: 0.7605 (mt0) cc_final: 0.7134 (mt0) REVERT: F 97 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7966 (mmtm) outliers start: 4 outliers final: 3 residues processed: 59 average time/residue: 0.2399 time to fit residues: 15.6868 Evaluate side-chains 60 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.173535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.130717 restraints weight = 2447.241| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 3.76 r_work: 0.4023 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2274 Z= 0.315 Angle : 0.562 4.380 3066 Z= 0.312 Chirality : 0.052 0.148 402 Planarity : 0.002 0.009 384 Dihedral : 5.722 16.622 324 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 6.14 % Allowed : 21.05 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.37 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.005 0.001 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.282 Fit side-chains REVERT: A 57 GLU cc_start: 0.8127 (tt0) cc_final: 0.7530 (tm-30) REVERT: A 58 LYS cc_start: 0.8018 (mmtp) cc_final: 0.7590 (tptm) REVERT: A 60 LYS cc_start: 0.8514 (mptt) cc_final: 0.8170 (mptt) REVERT: B 57 GLU cc_start: 0.7842 (tt0) cc_final: 0.7305 (tm-30) REVERT: B 58 LYS cc_start: 0.8042 (mmtp) cc_final: 0.7819 (tttt) REVERT: C 57 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7057 (tm-30) REVERT: C 97 LYS cc_start: 0.8617 (mmtp) cc_final: 0.5306 (pttm) REVERT: D 57 GLU cc_start: 0.7985 (tt0) cc_final: 0.7653 (tm-30) REVERT: D 97 LYS cc_start: 0.8554 (mmtp) cc_final: 0.8176 (mmtt) REVERT: E 62 GLN cc_start: 0.7457 (mt0) cc_final: 0.7053 (mt0) REVERT: F 57 GLU cc_start: 0.8367 (tt0) cc_final: 0.7579 (tm-30) REVERT: F 62 GLN cc_start: 0.7261 (mt0) cc_final: 0.6984 (mt0) outliers start: 14 outliers final: 13 residues processed: 78 average time/residue: 0.2043 time to fit residues: 17.8884 Evaluate side-chains 79 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 8 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.4536 r_free = 0.4536 target = 0.173501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.132315 restraints weight = 2487.992| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 3.74 r_work: 0.3953 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 2274 Z= 0.450 Angle : 0.676 5.131 3066 Z= 0.374 Chirality : 0.054 0.156 402 Planarity : 0.003 0.010 384 Dihedral : 6.266 17.449 324 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 9.21 % Allowed : 23.25 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.70 (0.37), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.28), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.005 0.001 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.238 Fit side-chains REVERT: A 57 GLU cc_start: 0.8152 (tt0) cc_final: 0.7416 (tm-30) REVERT: A 58 LYS cc_start: 0.7916 (mmtp) cc_final: 0.7480 (tptm) REVERT: A 60 LYS cc_start: 0.8499 (mptt) cc_final: 0.8222 (mptt) REVERT: B 57 GLU cc_start: 0.7780 (tt0) cc_final: 0.7206 (tm-30) REVERT: C 57 GLU cc_start: 0.7566 (tm-30) cc_final: 0.6991 (tm-30) REVERT: D 57 GLU cc_start: 0.7999 (tt0) cc_final: 0.7678 (tm-30) REVERT: D 98 ASP cc_start: 0.6803 (t0) cc_final: 0.6541 (t0) REVERT: E 57 GLU cc_start: 0.8384 (tt0) cc_final: 0.8098 (tm-30) REVERT: E 62 GLN cc_start: 0.7480 (mt0) cc_final: 0.7241 (mt0) REVERT: E 83 GLU cc_start: 0.8383 (mp0) cc_final: 0.8181 (mp0) REVERT: F 57 GLU cc_start: 0.8324 (tt0) cc_final: 0.7780 (tm-30) REVERT: F 58 LYS cc_start: 0.8113 (mmtp) cc_final: 0.7167 (mmmt) REVERT: F 97 LYS cc_start: 0.8382 (mmtp) cc_final: 0.8082 (mmtm) outliers start: 21 outliers final: 17 residues processed: 84 average time/residue: 0.1826 time to fit residues: 17.2744 Evaluate side-chains 92 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.4659 r_free = 0.4659 target = 0.182090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.142406 restraints weight = 2411.422| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 3.74 r_work: 0.4180 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2274 Z= 0.159 Angle : 0.499 4.538 3066 Z= 0.272 Chirality : 0.052 0.145 402 Planarity : 0.001 0.009 384 Dihedral : 5.133 14.834 324 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.26 % Allowed : 25.88 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.50 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 PHE 0.006 0.001 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.246 Fit side-chains REVERT: A 57 GLU cc_start: 0.8242 (tt0) cc_final: 0.7579 (tm-30) REVERT: A 58 LYS cc_start: 0.8004 (mmtp) cc_final: 0.7290 (mmmt) REVERT: A 60 LYS cc_start: 0.8553 (mptt) cc_final: 0.8284 (mptt) REVERT: B 45 LYS cc_start: 0.6017 (mmtt) cc_final: 0.5803 (mmtt) REVERT: B 58 LYS cc_start: 0.8214 (mmtp) cc_final: 0.7870 (mmmt) REVERT: C 57 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7415 (tm-30) REVERT: C 58 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8262 (mmtt) REVERT: D 83 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7858 (mt-10) REVERT: D 97 LYS cc_start: 0.8269 (mmtt) cc_final: 0.5587 (mtmt) REVERT: E 62 GLN cc_start: 0.7283 (mt0) cc_final: 0.6917 (mt0) REVERT: F 97 LYS cc_start: 0.8366 (mmtp) cc_final: 0.8124 (mmtm) outliers start: 12 outliers final: 10 residues processed: 73 average time/residue: 0.1887 time to fit residues: 15.4544 Evaluate side-chains 76 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.4524 r_free = 0.4524 target = 0.172154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.131993 restraints weight = 2529.963| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 3.72 r_work: 0.3959 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 2274 Z= 0.461 Angle : 0.670 6.303 3066 Z= 0.368 Chirality : 0.055 0.156 402 Planarity : 0.002 0.008 384 Dihedral : 6.040 18.164 324 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 8.77 % Allowed : 22.81 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.74 (0.37), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS F 50 PHE 0.006 0.002 PHE D 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.227 Fit side-chains REVERT: A 57 GLU cc_start: 0.8164 (tt0) cc_final: 0.7375 (tm-30) REVERT: A 58 LYS cc_start: 0.7879 (mmtp) cc_final: 0.7400 (mmtp) REVERT: A 60 LYS cc_start: 0.8426 (mptt) cc_final: 0.8194 (mptt) REVERT: B 57 GLU cc_start: 0.7945 (tt0) cc_final: 0.7686 (tm-30) REVERT: C 45 LYS cc_start: 0.2670 (tptp) cc_final: 0.2268 (tptp) REVERT: C 57 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7051 (tm-30) REVERT: D 83 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7967 (mt-10) REVERT: D 97 LYS cc_start: 0.8604 (mmtt) cc_final: 0.6189 (mtmt) REVERT: D 98 ASP cc_start: 0.6466 (t0) cc_final: 0.6137 (t0) REVERT: E 62 GLN cc_start: 0.7479 (mt0) cc_final: 0.7108 (mt0) REVERT: F 57 GLU cc_start: 0.8370 (tt0) cc_final: 0.7879 (tm-30) REVERT: F 58 LYS cc_start: 0.8089 (mmtp) cc_final: 0.7393 (mmmt) REVERT: F 97 LYS cc_start: 0.8357 (mmtp) cc_final: 0.8052 (mmtm) outliers start: 20 outliers final: 15 residues processed: 83 average time/residue: 0.1852 time to fit residues: 17.3641 Evaluate side-chains 91 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.4621 r_free = 0.4621 target = 0.179996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.140201 restraints weight = 2529.975| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 3.84 r_work: 0.4076 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2274 Z= 0.175 Angle : 0.519 5.190 3066 Z= 0.280 Chirality : 0.051 0.143 402 Planarity : 0.001 0.013 384 Dihedral : 5.108 14.996 324 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 6.14 % Allowed : 25.00 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.47 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.006 0.001 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.254 Fit side-chains REVERT: A 57 GLU cc_start: 0.8076 (tt0) cc_final: 0.7434 (tm-30) REVERT: A 58 LYS cc_start: 0.7887 (mmtp) cc_final: 0.7456 (mmmt) REVERT: A 60 LYS cc_start: 0.8496 (mptt) cc_final: 0.8278 (mptt) REVERT: B 45 LYS cc_start: 0.6260 (mmtt) cc_final: 0.6004 (mmtt) REVERT: B 57 GLU cc_start: 0.7998 (tt0) cc_final: 0.7703 (tm-30) REVERT: B 97 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7918 (mmtt) REVERT: C 45 LYS cc_start: 0.3044 (tptp) cc_final: 0.2630 (tptp) REVERT: C 57 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7227 (tm-30) REVERT: C 58 LYS cc_start: 0.8445 (mmtt) cc_final: 0.8190 (mmtt) REVERT: D 57 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7553 (tm-30) REVERT: D 83 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7884 (mt-10) REVERT: D 97 LYS cc_start: 0.8287 (mmtt) cc_final: 0.5498 (mtmt) REVERT: E 62 GLN cc_start: 0.7234 (mt0) cc_final: 0.6851 (mt0) REVERT: F 97 LYS cc_start: 0.8280 (mmtp) cc_final: 0.7970 (mmtm) outliers start: 14 outliers final: 12 residues processed: 80 average time/residue: 0.1858 time to fit residues: 16.7487 Evaluate side-chains 83 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 22 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.4541 r_free = 0.4541 target = 0.172815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.132773 restraints weight = 2520.827| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 3.75 r_work: 0.3971 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 2274 Z= 0.421 Angle : 0.646 5.259 3066 Z= 0.354 Chirality : 0.055 0.151 402 Planarity : 0.002 0.011 384 Dihedral : 5.785 17.474 324 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 7.46 % Allowed : 23.25 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.67 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS F 50 PHE 0.007 0.001 PHE D 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.233 Fit side-chains REVERT: A 57 GLU cc_start: 0.8098 (tt0) cc_final: 0.7374 (tm-30) REVERT: A 58 LYS cc_start: 0.7871 (mmtp) cc_final: 0.7425 (mmtp) REVERT: B 57 GLU cc_start: 0.8000 (tt0) cc_final: 0.7372 (tm-30) REVERT: C 45 LYS cc_start: 0.3245 (tptp) cc_final: 0.2926 (tptp) REVERT: C 57 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7067 (tm-30) REVERT: C 58 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8173 (mmtt) REVERT: D 57 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7554 (tm-30) REVERT: D 83 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7977 (mt-10) REVERT: D 97 LYS cc_start: 0.8573 (mmtt) cc_final: 0.6137 (mtmt) REVERT: E 57 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8064 (tm-30) REVERT: E 62 GLN cc_start: 0.7466 (mt0) cc_final: 0.7240 (mt0) REVERT: F 57 GLU cc_start: 0.8341 (tt0) cc_final: 0.7846 (tm-30) REVERT: F 58 LYS cc_start: 0.8139 (mmtp) cc_final: 0.7265 (mmmt) outliers start: 17 outliers final: 14 residues processed: 83 average time/residue: 0.1856 time to fit residues: 17.2761 Evaluate side-chains 90 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.4658 r_free = 0.4658 target = 0.182255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.144514 restraints weight = 2477.728| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 3.52 r_work: 0.3961 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 2274 Z= 0.449 Angle : 0.720 7.202 3066 Z= 0.390 Chirality : 0.056 0.160 402 Planarity : 0.002 0.010 384 Dihedral : 5.967 17.334 324 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 6.14 % Allowed : 25.00 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.86 (0.37), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.006 0.001 PHE D 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.280 Fit side-chains REVERT: A 57 GLU cc_start: 0.8081 (tt0) cc_final: 0.7319 (tm-30) REVERT: A 58 LYS cc_start: 0.7936 (mmtp) cc_final: 0.7568 (mmtp) REVERT: B 57 GLU cc_start: 0.7941 (tt0) cc_final: 0.7687 (tm-30) REVERT: C 57 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7113 (tm-30) REVERT: C 58 LYS cc_start: 0.8489 (mmtt) cc_final: 0.8257 (mmtt) REVERT: D 57 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7473 (tm-30) REVERT: D 83 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7952 (mt-10) REVERT: E 57 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7933 (tm-30) REVERT: E 62 GLN cc_start: 0.7431 (mt0) cc_final: 0.7100 (mt0) REVERT: F 57 GLU cc_start: 0.8324 (tt0) cc_final: 0.7988 (tm-30) REVERT: F 58 LYS cc_start: 0.8189 (mmtp) cc_final: 0.7425 (mmmt) outliers start: 14 outliers final: 14 residues processed: 86 average time/residue: 0.1790 time to fit residues: 17.5402 Evaluate side-chains 95 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 5 optimal weight: 30.0000 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.4574 r_free = 0.4574 target = 0.178980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.139791 restraints weight = 2521.933| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 3.73 r_work: 0.3982 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2274 Z= 0.297 Angle : 0.635 5.955 3066 Z= 0.341 Chirality : 0.053 0.152 402 Planarity : 0.002 0.024 384 Dihedral : 5.479 16.392 324 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 6.58 % Allowed : 23.25 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.79 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.004 0.001 PHE A 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1663.33 seconds wall clock time: 29 minutes 39.97 seconds (1779.97 seconds total)