Starting phenix.real_space_refine on Sun Mar 10 14:40:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l4s_0833/03_2024/6l4s_0833.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l4s_0833/03_2024/6l4s_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l4s_0833/03_2024/6l4s_0833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l4s_0833/03_2024/6l4s_0833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l4s_0833/03_2024/6l4s_0833.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l4s_0833/03_2024/6l4s_0833.pdb" } 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 Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2268 Number of models: 1 Model: "" Number of chains: 6 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} Chain: "B" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "C" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "D" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "E" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "F" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Time building chain proxies: 1.57, per 1000 atoms: 0.69 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 - 3.50 Amino acid : False - 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: 0.85 Conformation dependent library (CDL) restraints added in 426.8 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: 0.28 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: 0.46 Time building geometry restraints manager: 0.93 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: 103.77 - 109.29: 370 109.29 - 114.81: 1120 114.81 - 120.32: 744 120.32 - 125.84: 826 125.84 - 131.35: 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 2.440 nonbonded pdb=" OG1 THR B 54 " pdb=" OG1 THR F 64 " model vdw 2.459 2.440 nonbonded pdb=" OG1 THR B 64 " pdb=" OG1 THR D 54 " model vdw 2.510 2.440 nonbonded pdb=" OD1 ASP A 98 " pdb=" N GLN A 99 " model vdw 2.524 2.520 nonbonded pdb=" OD1 ASP F 98 " pdb=" N GLN F 99 " model vdw 2.524 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 0.180 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: 0.980 Check model and map are aligned: 0.070 Set scattering table: 0.020 Process input model: 11.030 Find NCS groups from input model: 0.160 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.200 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.247 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: 0.2198 time to fit residues: 18.6964 Evaluate side-chains 77 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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: 8.9990 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2274 Z= 0.190 Angle : 0.563 4.367 3066 Z= 0.313 Chirality : 0.051 0.154 402 Planarity : 0.002 0.016 384 Dihedral : 5.970 16.420 324 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.63 % Allowed : 19.74 % Favored : 77.63 % 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: -3.31 (0.37), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.010 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 75 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.250 Fit side-chains REVERT: A 57 GLU cc_start: 0.7495 (tt0) cc_final: 0.7097 (tm-30) REVERT: A 58 LYS cc_start: 0.7240 (mmtp) cc_final: 0.6710 (tptm) REVERT: A 96 LYS cc_start: 0.7295 (mtpm) cc_final: 0.6673 (mttt) REVERT: A 97 LYS cc_start: 0.7412 (mmtt) cc_final: 0.7162 (mmtp) REVERT: B 57 GLU cc_start: 0.7181 (tt0) cc_final: 0.6715 (tm-30) REVERT: B 97 LYS cc_start: 0.7610 (mmtt) cc_final: 0.7335 (mmtt) REVERT: C 57 GLU cc_start: 0.7398 (tt0) cc_final: 0.7062 (tm-30) REVERT: C 58 LYS cc_start: 0.8540 (mmtp) cc_final: 0.8327 (mmtt) REVERT: D 57 GLU cc_start: 0.7466 (tt0) cc_final: 0.7063 (tm-30) REVERT: D 96 LYS cc_start: 0.7644 (mtpm) cc_final: 0.6844 (mttt) REVERT: E 62 GLN cc_start: 0.6844 (mt0) cc_final: 0.6444 (mt0) REVERT: F 45 LYS cc_start: 0.5451 (mmtt) cc_final: 0.5160 (mmtm) REVERT: F 57 GLU cc_start: 0.8013 (tt0) cc_final: 0.7304 (tm-30) REVERT: F 58 LYS cc_start: 0.7521 (mmtp) cc_final: 0.6672 (mmmt) REVERT: F 59 THR cc_start: 0.8397 (m) cc_final: 0.7938 (t) REVERT: F 62 GLN cc_start: 0.7152 (mt0) cc_final: 0.6461 (mt0) REVERT: F 97 LYS cc_start: 0.7067 (mmtt) cc_final: 0.6587 (mmtm) outliers start: 6 outliers final: 6 residues processed: 74 average time/residue: 0.2868 time to fit residues: 23.5901 Evaluate side-chains 69 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 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 22 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 2274 Z= 0.311 Angle : 0.591 4.078 3066 Z= 0.330 Chirality : 0.052 0.160 402 Planarity : 0.002 0.012 384 Dihedral : 6.100 16.755 324 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 6.58 % Allowed : 21.49 % 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: -3.42 (0.37), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.28), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 PHE 0.007 0.002 PHE A 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 87 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.246 Fit side-chains REVERT: A 57 GLU cc_start: 0.7605 (tt0) cc_final: 0.6839 (tm-30) REVERT: A 58 LYS cc_start: 0.7446 (mmtp) cc_final: 0.6934 (tptm) REVERT: A 97 LYS cc_start: 0.7685 (mmtt) cc_final: 0.7390 (mmtm) REVERT: B 58 LYS cc_start: 0.6838 (tttt) cc_final: 0.6627 (tttt) REVERT: C 57 GLU cc_start: 0.7325 (tt0) cc_final: 0.6959 (tm-30) REVERT: C 58 LYS cc_start: 0.8498 (mmtp) cc_final: 0.8295 (mmtt) REVERT: D 57 GLU cc_start: 0.7349 (tt0) cc_final: 0.6905 (tm-30) REVERT: D 97 LYS cc_start: 0.8434 (mmtp) cc_final: 0.8035 (mmtt) REVERT: F 57 GLU cc_start: 0.7932 (tt0) cc_final: 0.7350 (tm-30) REVERT: F 58 LYS cc_start: 0.7600 (mmtp) cc_final: 0.7226 (mmtp) REVERT: F 59 THR cc_start: 0.8291 (m) cc_final: 0.7866 (t) REVERT: F 62 GLN cc_start: 0.7003 (mt0) cc_final: 0.6398 (mt0) outliers start: 15 outliers final: 14 residues processed: 79 average time/residue: 0.2013 time to fit residues: 17.7267 Evaluate side-chains 81 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 59 THR 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 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 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 2274 Z= 0.429 Angle : 0.681 4.999 3066 Z= 0.377 Chirality : 0.054 0.162 402 Planarity : 0.003 0.011 384 Dihedral : 6.456 18.281 324 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 9.65 % Allowed : 20.18 % 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: -3.80 (0.37), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.28), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.006 0.002 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 98 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 0.259 Fit side-chains REVERT: A 57 GLU cc_start: 0.7550 (tt0) cc_final: 0.6729 (tm-30) REVERT: A 58 LYS cc_start: 0.7517 (mmtp) cc_final: 0.6937 (tptm) REVERT: A 97 LYS cc_start: 0.7528 (mmtt) cc_final: 0.7280 (mmtm) REVERT: B 58 LYS cc_start: 0.7025 (tttt) cc_final: 0.6755 (tttt) REVERT: B 97 LYS cc_start: 0.7607 (mmtt) cc_final: 0.7263 (mmtt) REVERT: C 57 GLU cc_start: 0.7169 (tt0) cc_final: 0.6944 (tm-30) REVERT: D 45 LYS cc_start: 0.2306 (tptt) cc_final: 0.2088 (tptp) REVERT: D 57 GLU cc_start: 0.7253 (tt0) cc_final: 0.7021 (tm-30) REVERT: E 57 GLU cc_start: 0.8174 (tt0) cc_final: 0.7734 (tm-30) REVERT: E 62 GLN cc_start: 0.6808 (mt0) cc_final: 0.6362 (mt0) REVERT: F 57 GLU cc_start: 0.7907 (tt0) cc_final: 0.7299 (tm-30) REVERT: F 58 LYS cc_start: 0.7429 (mmtp) cc_final: 0.6802 (mmmt) REVERT: F 59 THR cc_start: 0.8185 (m) cc_final: 0.7793 (t) REVERT: F 62 GLN cc_start: 0.6978 (mt0) cc_final: 0.6537 (mt0) REVERT: F 97 LYS cc_start: 0.7815 (mmtp) cc_final: 0.7496 (mmtm) outliers start: 22 outliers final: 18 residues processed: 86 average time/residue: 0.1933 time to fit residues: 18.6047 Evaluate side-chains 90 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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 59 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 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 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2274 Z= 0.210 Angle : 0.522 4.157 3066 Z= 0.289 Chirality : 0.052 0.148 402 Planarity : 0.002 0.010 384 Dihedral : 5.422 15.093 324 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 8.33 % Allowed : 20.18 % Favored : 71.49 % 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 (0.38), 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 0.000 HIS F 50 PHE 0.006 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 87 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 68 time to evaluate : 0.261 Fit side-chains REVERT: A 57 GLU cc_start: 0.7529 (tt0) cc_final: 0.6832 (tm-30) REVERT: A 58 LYS cc_start: 0.7411 (mmtp) cc_final: 0.6843 (mmmt) REVERT: A 97 LYS cc_start: 0.7454 (mmtt) cc_final: 0.7224 (mmtm) REVERT: B 58 LYS cc_start: 0.6942 (tttt) cc_final: 0.6432 (tttt) REVERT: D 57 GLU cc_start: 0.7350 (tt0) cc_final: 0.7100 (tm-30) REVERT: D 83 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7644 (mt-10) REVERT: E 62 GLN cc_start: 0.6809 (mt0) cc_final: 0.6328 (mt0) REVERT: F 57 GLU cc_start: 0.7943 (tt0) cc_final: 0.7292 (tm-30) REVERT: F 58 LYS cc_start: 0.7572 (mmtp) cc_final: 0.6988 (mmmt) REVERT: F 62 GLN cc_start: 0.7033 (mt0) cc_final: 0.6503 (mt0) REVERT: F 97 LYS cc_start: 0.7378 (mmtp) cc_final: 0.6991 (mmtm) outliers start: 19 outliers final: 13 residues processed: 80 average time/residue: 0.2026 time to fit residues: 18.0383 Evaluate side-chains 83 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 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 52 VAL 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 7 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 21 optimal weight: 0.3980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.4408 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= 0.114 Angle : 0.452 3.850 3066 Z= 0.247 Chirality : 0.051 0.140 402 Planarity : 0.001 0.009 384 Dihedral : 4.669 14.709 324 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.95 % Allowed : 24.56 % Favored : 71.49 % 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: -3.39 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS C 50 PHE 0.005 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 84 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.251 Fit side-chains REVERT: A 57 GLU cc_start: 0.7434 (tt0) cc_final: 0.6800 (tm-30) REVERT: A 58 LYS cc_start: 0.7321 (mmtp) cc_final: 0.6956 (mmmt) REVERT: B 58 LYS cc_start: 0.7085 (tttt) cc_final: 0.6493 (mtpt) REVERT: C 57 GLU cc_start: 0.6762 (tm-30) cc_final: 0.6252 (tm-30) REVERT: C 58 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7768 (mmtt) REVERT: D 45 LYS cc_start: 0.2117 (tptt) cc_final: 0.1871 (tptp) REVERT: D 57 GLU cc_start: 0.7315 (tt0) cc_final: 0.7048 (tm-30) REVERT: D 83 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7551 (mt-10) REVERT: D 97 LYS cc_start: 0.7911 (mmtt) cc_final: 0.5314 (mtmt) REVERT: E 62 GLN cc_start: 0.6533 (mt0) cc_final: 0.6331 (mt0) REVERT: F 49 VAL cc_start: 0.7515 (m) cc_final: 0.7153 (t) REVERT: F 62 GLN cc_start: 0.7003 (mt0) cc_final: 0.6695 (mt0) REVERT: F 97 LYS cc_start: 0.7022 (mmtp) cc_final: 0.6738 (mmtm) outliers start: 9 outliers final: 9 residues processed: 79 average time/residue: 0.2014 time to fit residues: 17.7811 Evaluate side-chains 82 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 72 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.0370 chunk 24 optimal weight: 0.0370 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 overall best weight: 2.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2274 Z= 0.230 Angle : 0.533 5.928 3066 Z= 0.288 Chirality : 0.051 0.145 402 Planarity : 0.001 0.007 384 Dihedral : 4.993 14.705 324 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 8.33 % Allowed : 21.49 % 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: -3.39 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.004 0.001 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 91 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 0.247 Fit side-chains REVERT: A 57 GLU cc_start: 0.7446 (tt0) cc_final: 0.6787 (tm-30) REVERT: A 58 LYS cc_start: 0.7168 (mmtp) cc_final: 0.6779 (mmmt) REVERT: A 97 LYS cc_start: 0.8029 (mmtm) cc_final: 0.7613 (mmtm) REVERT: B 58 LYS cc_start: 0.6871 (tttt) cc_final: 0.6453 (tttt) REVERT: C 57 GLU cc_start: 0.6806 (tm-30) cc_final: 0.6304 (tm-30) REVERT: C 58 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7603 (mmtt) REVERT: D 45 LYS cc_start: 0.2063 (tptt) cc_final: 0.1839 (tptp) REVERT: D 83 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7608 (mt-10) REVERT: D 97 LYS cc_start: 0.8099 (mmtt) cc_final: 0.6062 (mtmt) REVERT: E 62 GLN cc_start: 0.6527 (mt0) cc_final: 0.6024 (mt0) REVERT: E 83 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8177 (mp0) REVERT: F 57 GLU cc_start: 0.8053 (tt0) cc_final: 0.7186 (tm-30) outliers start: 19 outliers final: 14 residues processed: 80 average time/residue: 0.1786 time to fit residues: 16.0813 Evaluate side-chains 85 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 62 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 72 THR 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 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 2 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2274 Z= 0.294 Angle : 0.572 5.146 3066 Z= 0.312 Chirality : 0.052 0.153 402 Planarity : 0.002 0.007 384 Dihedral : 5.325 15.150 324 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 7.89 % Allowed : 21.93 % 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: -3.49 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 PHE 0.004 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 105 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.255 Fit side-chains REVERT: A 57 GLU cc_start: 0.7420 (tt0) cc_final: 0.6710 (tm-30) REVERT: A 58 LYS cc_start: 0.7216 (mmtp) cc_final: 0.6785 (mmmt) REVERT: A 83 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7699 (mp0) REVERT: B 58 LYS cc_start: 0.6767 (tttt) cc_final: 0.6534 (tttt) REVERT: B 97 LYS cc_start: 0.7786 (mmtt) cc_final: 0.7571 (mmtp) REVERT: C 45 LYS cc_start: 0.2040 (tptp) cc_final: 0.1760 (tptp) REVERT: C 57 GLU cc_start: 0.6820 (tm-30) cc_final: 0.6349 (tm-30) REVERT: C 98 ASP cc_start: 0.6640 (t0) cc_final: 0.6410 (t0) REVERT: D 57 GLU cc_start: 0.6831 (tm-30) cc_final: 0.6406 (tm-30) REVERT: D 83 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7673 (mt-10) REVERT: D 97 LYS cc_start: 0.8273 (mmtt) cc_final: 0.6206 (mtmt) REVERT: E 57 GLU cc_start: 0.8074 (tt0) cc_final: 0.7697 (tm-30) REVERT: E 62 GLN cc_start: 0.6796 (mt0) cc_final: 0.6305 (mt0) REVERT: F 57 GLU cc_start: 0.7931 (tt0) cc_final: 0.7435 (tm-30) REVERT: F 58 LYS cc_start: 0.7405 (mmtp) cc_final: 0.6829 (mmmt) REVERT: F 97 LYS cc_start: 0.7209 (mmtp) cc_final: 0.6680 (mmtm) outliers start: 18 outliers final: 17 residues processed: 90 average time/residue: 0.1775 time to fit residues: 18.0402 Evaluate side-chains 103 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 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 62 GLN 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 D residue 49 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 72 THR 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 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 28 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 25 optimal weight: 0.0170 overall best weight: 2.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2274 Z= 0.214 Angle : 0.548 4.829 3066 Z= 0.294 Chirality : 0.052 0.146 402 Planarity : 0.001 0.008 384 Dihedral : 5.015 14.350 324 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 7.89 % Allowed : 21.05 % Favored : 71.05 % 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: -3.48 (0.40), 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 0.005 0.001 PHE A 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 97 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.267 Fit side-chains REVERT: A 45 LYS cc_start: 0.5191 (mmtt) cc_final: 0.4919 (mmtt) REVERT: A 57 GLU cc_start: 0.7405 (tt0) cc_final: 0.6784 (tm-30) REVERT: A 58 LYS cc_start: 0.7232 (mmtp) cc_final: 0.6866 (mmmt) REVERT: A 83 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7688 (mp0) REVERT: A 97 LYS cc_start: 0.7686 (mmtt) cc_final: 0.7371 (mmtm) REVERT: B 58 LYS cc_start: 0.6748 (tttt) cc_final: 0.6414 (tttt) REVERT: B 97 LYS cc_start: 0.7884 (mmtt) cc_final: 0.7626 (mmtp) REVERT: C 57 GLU cc_start: 0.6829 (tm-30) cc_final: 0.6444 (tm-30) REVERT: C 96 LYS cc_start: 0.7621 (mmmm) cc_final: 0.6960 (mttt) REVERT: D 57 GLU cc_start: 0.6827 (tm-30) cc_final: 0.6397 (tm-30) REVERT: D 83 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7642 (mt-10) REVERT: D 97 LYS cc_start: 0.8211 (mmtt) cc_final: 0.6102 (mtmt) REVERT: E 62 GLN cc_start: 0.6824 (mt0) cc_final: 0.6357 (mt0) REVERT: F 57 GLU cc_start: 0.7982 (tt0) cc_final: 0.7292 (tm-30) REVERT: F 97 LYS cc_start: 0.7183 (mmtp) cc_final: 0.6653 (mmtm) outliers start: 18 outliers final: 18 residues processed: 85 average time/residue: 0.1801 time to fit residues: 17.2514 Evaluate side-chains 96 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 62 GLN 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 D residue 49 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 72 THR 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 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 7 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2274 Z= 0.231 Angle : 0.554 4.762 3066 Z= 0.299 Chirality : 0.052 0.148 402 Planarity : 0.001 0.008 384 Dihedral : 5.019 14.424 324 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 7.89 % Allowed : 21.49 % Favored : 70.61 % 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: -3.49 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.30), 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 ********************** 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 98 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.265 Fit side-chains REVERT: A 57 GLU cc_start: 0.7402 (tt0) cc_final: 0.6757 (tm-30) REVERT: A 58 LYS cc_start: 0.7233 (mmtp) cc_final: 0.6825 (mmmt) REVERT: A 83 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7772 (mp0) REVERT: B 58 LYS cc_start: 0.6813 (tttt) cc_final: 0.6507 (tttt) REVERT: B 97 LYS cc_start: 0.7782 (mmtt) cc_final: 0.7551 (mmtp) REVERT: C 57 GLU cc_start: 0.6863 (tm-30) cc_final: 0.6382 (tm-30) REVERT: C 83 GLU cc_start: 0.7683 (mp0) cc_final: 0.7299 (mp0) REVERT: C 97 LYS cc_start: 0.8109 (mmtt) cc_final: 0.5181 (pttm) REVERT: D 57 GLU cc_start: 0.6818 (tm-30) cc_final: 0.6387 (tm-30) REVERT: D 83 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7644 (mt-10) REVERT: D 97 LYS cc_start: 0.8202 (mmtt) cc_final: 0.6239 (mtmt) REVERT: E 62 GLN cc_start: 0.6835 (mt0) cc_final: 0.6372 (mt0) REVERT: F 57 GLU cc_start: 0.7941 (tt0) cc_final: 0.7460 (tm-30) REVERT: F 58 LYS cc_start: 0.7477 (mmtp) cc_final: 0.6889 (mmmt) REVERT: F 97 LYS cc_start: 0.7219 (mmtp) cc_final: 0.6659 (mmtm) outliers start: 18 outliers final: 18 residues processed: 84 average time/residue: 0.1840 time to fit residues: 17.3443 Evaluate side-chains 97 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 62 GLN 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 D residue 49 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 72 THR 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 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 27 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 0.2980 chunk 17 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 20.0000 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 = 0.4573 r_free = 0.4573 target = 0.176214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.133861 restraints weight = 2525.882| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 3.72 r_work: 0.4032 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2274 Z= 0.207 Angle : 0.549 6.703 3066 Z= 0.293 Chirality : 0.052 0.147 402 Planarity : 0.001 0.008 384 Dihedral : 4.887 14.160 324 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 7.89 % Allowed : 21.49 % Favored : 70.61 % 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: -3.41 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.005 0.001 PHE A 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 984.25 seconds wall clock time: 19 minutes 5.68 seconds (1145.68 seconds total)