Starting phenix.real_space_refine on Wed Jan 17 12:16:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkt_21708/01_2024/6wkt_21708.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkt_21708/01_2024/6wkt_21708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkt_21708/01_2024/6wkt_21708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkt_21708/01_2024/6wkt_21708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkt_21708/01_2024/6wkt_21708.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkt_21708/01_2024/6wkt_21708.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 1884 2.51 5 N 556 2.21 5 O 620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 6": "OE1" <-> "OE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "B TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "C TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "D TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 44": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 3152 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "B" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "C" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "D" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Time building chain proxies: 2.28, per 1000 atoms: 0.72 Number of scatterers: 3152 At special positions: 0 Unit cell: (79.056, 63.504, 55.728, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 620 8.00 N 556 7.00 C 1884 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: 1.07 Conformation dependent library (CDL) restraints added in 522.8 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 85.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 5 through 29 removed outlier: 3.742A pdb=" N GLU A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 58 Processing helix chain 'A' and resid 62 through 82 Processing helix chain 'A' and resid 86 through 107 Processing helix chain 'B' and resid 5 through 29 removed outlier: 3.742A pdb=" N GLU B 29 " --> pdb=" O LYS B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 58 Processing helix chain 'B' and resid 62 through 82 Processing helix chain 'B' and resid 86 through 107 Processing helix chain 'C' and resid 5 through 29 removed outlier: 3.742A pdb=" N GLU C 29 " --> pdb=" O LYS C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 58 Processing helix chain 'C' and resid 62 through 82 Processing helix chain 'C' and resid 86 through 107 Processing helix chain 'D' and resid 5 through 29 removed outlier: 3.742A pdb=" N GLU D 29 " --> pdb=" O LYS D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 58 Processing helix chain 'D' and resid 62 through 82 Processing helix chain 'D' and resid 86 through 107 296 hydrogen bonds defined for protein. 888 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: 0.86 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 884 1.34 - 1.46: 504 1.46 - 1.58: 1696 1.58 - 1.70: 0 1.70 - 1.82: 108 Bond restraints: 3192 Sorted by residual: bond pdb=" C ILE B 39 " pdb=" N ARG B 40 " ideal model delta sigma weight residual 1.335 1.298 0.037 1.31e-02 5.83e+03 8.03e+00 bond pdb=" C ILE A 39 " pdb=" N ARG A 40 " ideal model delta sigma weight residual 1.335 1.298 0.037 1.31e-02 5.83e+03 8.03e+00 bond pdb=" C ILE D 39 " pdb=" N ARG D 40 " ideal model delta sigma weight residual 1.335 1.298 0.037 1.31e-02 5.83e+03 8.03e+00 bond pdb=" C ILE C 39 " pdb=" N ARG C 40 " ideal model delta sigma weight residual 1.335 1.298 0.037 1.31e-02 5.83e+03 8.03e+00 bond pdb=" C THR C 24 " pdb=" O THR C 24 " ideal model delta sigma weight residual 1.237 1.216 0.021 1.17e-02 7.31e+03 3.08e+00 ... (remaining 3187 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.37: 56 106.37 - 112.61: 1616 112.61 - 118.85: 1004 118.85 - 125.09: 1568 125.09 - 131.33: 40 Bond angle restraints: 4284 Sorted by residual: angle pdb=" C GLN D 32 " pdb=" N HIS D 33 " pdb=" CA HIS D 33 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C GLN B 32 " pdb=" N HIS B 33 " pdb=" CA HIS B 33 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C GLN A 32 " pdb=" N HIS A 33 " pdb=" CA HIS A 33 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C GLN C 32 " pdb=" N HIS C 33 " pdb=" CA HIS C 33 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" O ILE D 39 " pdb=" C ILE D 39 " pdb=" N ARG D 40 " ideal model delta sigma weight residual 121.90 118.01 3.89 1.04e+00 9.25e-01 1.40e+01 ... (remaining 4279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 1820 17.75 - 35.49: 136 35.49 - 53.23: 24 53.23 - 70.97: 0 70.97 - 88.72: 8 Dihedral angle restraints: 1988 sinusoidal: 740 harmonic: 1248 Sorted by residual: dihedral pdb=" CA SER A 36 " pdb=" C SER A 36 " pdb=" N GLY A 37 " pdb=" CA GLY A 37 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA SER B 36 " pdb=" C SER B 36 " pdb=" N GLY B 37 " pdb=" CA GLY B 37 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA SER D 36 " pdb=" C SER D 36 " pdb=" N GLY D 37 " pdb=" CA GLY D 37 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 1985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 280 0.034 - 0.068: 148 0.068 - 0.102: 36 0.102 - 0.136: 12 0.136 - 0.170: 4 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA THR D 24 " pdb=" N THR D 24 " pdb=" C THR D 24 " pdb=" CB THR D 24 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA THR C 24 " pdb=" N THR C 24 " pdb=" C THR C 24 " pdb=" CB THR C 24 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA THR B 24 " pdb=" N THR B 24 " pdb=" C THR B 24 " pdb=" CB THR B 24 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 477 not shown) Planarity restraints: 568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 84 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C HIS B 84 " 0.049 2.00e-02 2.50e+03 pdb=" O HIS B 84 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP B 85 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 84 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C HIS D 84 " -0.049 2.00e-02 2.50e+03 pdb=" O HIS D 84 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP D 85 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 84 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C HIS C 84 " 0.049 2.00e-02 2.50e+03 pdb=" O HIS C 84 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP C 85 " -0.016 2.00e-02 2.50e+03 ... (remaining 565 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1012 2.84 - 3.36: 3094 3.36 - 3.87: 5334 3.87 - 4.39: 5872 4.39 - 4.90: 10766 Nonbonded interactions: 26078 Sorted by model distance: nonbonded pdb=" O LYS D 54 " pdb=" OG1 THR D 58 " model vdw 2.329 2.440 nonbonded pdb=" O LYS B 54 " pdb=" OG1 THR B 58 " model vdw 2.329 2.440 nonbonded pdb=" O LYS A 54 " pdb=" OG1 THR A 58 " model vdw 2.329 2.440 nonbonded pdb=" O LYS C 54 " pdb=" OG1 THR C 58 " model vdw 2.329 2.440 nonbonded pdb=" O GLU B 75 " pdb=" OG1 THR B 79 " model vdw 2.426 2.440 ... (remaining 26073 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' } 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: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.040 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.004 0.037 3192 Z= 0.298 Angle : 0.808 8.085 4284 Z= 0.490 Chirality : 0.046 0.170 480 Planarity : 0.006 0.029 568 Dihedral : 13.975 88.716 1164 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.29), residues: 416 helix: -1.91 (0.19), residues: 368 sheet: None (None), residues: 0 loop : -3.11 (0.74), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 34 PHE 0.016 0.003 PHE A 23 TYR 0.006 0.002 TYR A 4 ARG 0.001 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.363 Fit side-chains REVERT: A 16 MET cc_start: 0.7205 (mtp) cc_final: 0.6914 (mtm) REVERT: A 80 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6400 (mm-30) REVERT: A 90 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8491 (mm-40) REVERT: B 16 MET cc_start: 0.7189 (mtp) cc_final: 0.6892 (mtm) REVERT: B 80 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6403 (mm-30) REVERT: B 90 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8495 (mm-40) REVERT: C 16 MET cc_start: 0.7198 (mtp) cc_final: 0.6894 (mtm) REVERT: C 80 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6407 (mm-30) REVERT: C 90 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8494 (mm-40) REVERT: D 16 MET cc_start: 0.7207 (mtp) cc_final: 0.6907 (mtm) REVERT: D 80 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6408 (mm-30) REVERT: D 90 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8496 (mm-40) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2423 time to fit residues: 21.0460 Evaluate side-chains 64 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.7317 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3192 Z= 0.157 Angle : 0.453 4.195 4284 Z= 0.251 Chirality : 0.032 0.098 480 Planarity : 0.003 0.022 568 Dihedral : 4.145 12.698 440 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 16.09 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.36), residues: 416 helix: 0.84 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -2.63 (0.64), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 88 PHE 0.007 0.002 PHE D 62 TYR 0.004 0.001 TYR B 4 ARG 0.005 0.001 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.329 Fit side-chains REVERT: A 80 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6410 (mm-30) REVERT: B 44 GLU cc_start: 0.7972 (tp30) cc_final: 0.7770 (mm-30) REVERT: B 80 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6415 (mm-30) REVERT: C 80 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6413 (mm-30) REVERT: D 44 GLU cc_start: 0.7973 (tp30) cc_final: 0.7773 (mm-30) REVERT: D 80 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6414 (mm-30) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1612 time to fit residues: 14.8357 Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.7320 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3192 Z= 0.199 Angle : 0.470 4.510 4284 Z= 0.260 Chirality : 0.034 0.103 480 Planarity : 0.003 0.020 568 Dihedral : 3.989 13.248 440 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 18.39 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.38), residues: 416 helix: 1.81 (0.25), residues: 360 sheet: None (None), residues: 0 loop : -1.94 (0.68), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 88 PHE 0.011 0.002 PHE B 62 TYR 0.005 0.001 TYR B 4 ARG 0.005 0.001 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.455 Fit side-chains REVERT: A 80 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6736 (mm-30) REVERT: B 80 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6736 (mm-30) REVERT: C 80 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6739 (mm-30) REVERT: D 80 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6739 (mm-30) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1661 time to fit residues: 14.3703 Evaluate side-chains 75 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.7249 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3192 Z= 0.138 Angle : 0.442 4.144 4284 Z= 0.247 Chirality : 0.033 0.094 480 Planarity : 0.003 0.022 568 Dihedral : 3.860 12.902 440 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.15 % Allowed : 16.09 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.38), residues: 416 helix: 2.41 (0.25), residues: 360 sheet: None (None), residues: 0 loop : -1.60 (0.71), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 34 PHE 0.008 0.002 PHE C 23 TYR 0.004 0.001 TYR D 4 ARG 0.006 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.311 Fit side-chains REVERT: A 80 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6724 (mm-30) REVERT: B 80 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6727 (mm-30) REVERT: C 80 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6726 (mm-30) REVERT: D 80 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6731 (mm-30) outliers start: 4 outliers final: 0 residues processed: 72 average time/residue: 0.1628 time to fit residues: 14.0443 Evaluate side-chains 72 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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: 0.7306 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3192 Z= 0.187 Angle : 0.449 4.158 4284 Z= 0.251 Chirality : 0.034 0.099 480 Planarity : 0.003 0.021 568 Dihedral : 3.790 13.053 440 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 17.24 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.38), residues: 416 helix: 2.58 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -1.32 (0.76), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 34 PHE 0.010 0.002 PHE A 62 TYR 0.005 0.001 TYR D 4 ARG 0.006 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.331 Fit side-chains REVERT: A 75 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7094 (mm-30) REVERT: A 80 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6777 (mm-30) REVERT: B 75 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7096 (mm-30) REVERT: B 80 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6783 (mm-30) REVERT: C 75 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7095 (mm-30) REVERT: C 80 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6783 (mm-30) REVERT: D 75 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7090 (mm-30) REVERT: D 80 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6786 (mm-30) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1632 time to fit residues: 14.1086 Evaluate side-chains 72 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 37 optimal weight: 0.0470 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.2084 ------------------------------------------------------------------------------- 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: 0.7286 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3192 Z= 0.157 Angle : 0.425 4.119 4284 Z= 0.238 Chirality : 0.033 0.098 480 Planarity : 0.002 0.012 568 Dihedral : 3.726 12.930 440 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 17.24 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.38), residues: 416 helix: 2.84 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -1.08 (0.79), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 34 PHE 0.010 0.002 PHE B 62 TYR 0.005 0.001 TYR A 4 ARG 0.001 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.438 Fit side-chains REVERT: A 75 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7106 (mm-30) REVERT: A 80 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6790 (mm-30) REVERT: B 75 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7109 (mm-30) REVERT: B 80 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6843 (mm-30) REVERT: C 75 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7105 (mm-30) REVERT: C 80 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6795 (mm-30) REVERT: D 75 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7110 (mm-30) REVERT: D 80 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6850 (mm-30) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1678 time to fit residues: 14.5187 Evaluate side-chains 72 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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: 0.7325 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3192 Z= 0.211 Angle : 0.471 4.094 4284 Z= 0.261 Chirality : 0.035 0.101 480 Planarity : 0.002 0.016 568 Dihedral : 3.813 12.964 440 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 17.82 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.44 (0.38), residues: 416 helix: 2.72 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -0.91 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 88 PHE 0.011 0.002 PHE D 62 TYR 0.005 0.001 TYR C 4 ARG 0.006 0.001 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.309 Fit side-chains REVERT: A 59 ASP cc_start: 0.7817 (t0) cc_final: 0.7249 (t70) REVERT: A 80 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6842 (mm-30) REVERT: B 59 ASP cc_start: 0.7812 (t0) cc_final: 0.7254 (t70) REVERT: B 80 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6846 (mm-30) REVERT: C 59 ASP cc_start: 0.7821 (t0) cc_final: 0.7264 (t70) REVERT: C 80 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6845 (mm-30) REVERT: D 59 ASP cc_start: 0.7822 (t0) cc_final: 0.7258 (t70) REVERT: D 80 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6849 (mm-30) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1606 time to fit residues: 13.9282 Evaluate side-chains 72 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 0.0070 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 0.0970 chunk 11 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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: 0.7232 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3192 Z= 0.120 Angle : 0.410 4.007 4284 Z= 0.232 Chirality : 0.032 0.096 480 Planarity : 0.003 0.025 568 Dihedral : 3.618 12.810 440 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.15 % Allowed : 17.24 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.07 (0.38), residues: 416 helix: 3.14 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -0.71 (0.84), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 34 PHE 0.009 0.002 PHE C 23 TYR 0.004 0.001 TYR A 4 ARG 0.007 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.378 Fit side-chains REVERT: A 59 ASP cc_start: 0.7768 (t0) cc_final: 0.7319 (t70) REVERT: A 75 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7215 (mm-30) REVERT: A 80 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6772 (mm-30) REVERT: B 59 ASP cc_start: 0.7760 (t0) cc_final: 0.7310 (t70) REVERT: B 75 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7206 (mm-30) REVERT: B 80 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6778 (mm-30) REVERT: C 59 ASP cc_start: 0.7776 (t0) cc_final: 0.7328 (t70) REVERT: C 75 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7210 (mm-30) REVERT: C 80 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6781 (mm-30) REVERT: D 59 ASP cc_start: 0.7770 (t0) cc_final: 0.7323 (t70) REVERT: D 75 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7210 (mm-30) REVERT: D 80 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6785 (mm-30) outliers start: 4 outliers final: 0 residues processed: 80 average time/residue: 0.1623 time to fit residues: 15.8264 Evaluate side-chains 72 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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: 0.7251 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3192 Z= 0.165 Angle : 0.495 6.654 4284 Z= 0.253 Chirality : 0.033 0.099 480 Planarity : 0.003 0.022 568 Dihedral : 3.470 11.515 440 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 17.24 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.14 (0.38), residues: 416 helix: 3.19 (0.24), residues: 360 sheet: None (None), residues: 0 loop : -0.70 (0.86), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 34 PHE 0.008 0.002 PHE B 23 TYR 0.005 0.001 TYR C 4 ARG 0.007 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.329 Fit side-chains REVERT: A 59 ASP cc_start: 0.7837 (t0) cc_final: 0.7306 (t70) REVERT: A 80 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6826 (mm-30) REVERT: B 59 ASP cc_start: 0.7834 (t0) cc_final: 0.7316 (t70) REVERT: B 80 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6826 (mm-30) REVERT: C 59 ASP cc_start: 0.7838 (t0) cc_final: 0.7311 (t70) REVERT: C 80 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6829 (mm-30) REVERT: D 59 ASP cc_start: 0.7840 (t0) cc_final: 0.7310 (t70) REVERT: D 80 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6834 (mm-30) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1712 time to fit residues: 13.9526 Evaluate side-chains 68 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 0.0030 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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: 0.7236 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3192 Z= 0.130 Angle : 0.478 6.907 4284 Z= 0.243 Chirality : 0.033 0.098 480 Planarity : 0.003 0.026 568 Dihedral : 3.433 11.652 440 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 17.24 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.29 (0.37), residues: 416 helix: 3.28 (0.23), residues: 360 sheet: None (None), residues: 0 loop : -0.59 (0.88), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 34 PHE 0.009 0.002 PHE B 23 TYR 0.004 0.001 TYR A 4 ARG 0.007 0.001 ARG A 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.368 Fit side-chains REVERT: A 59 ASP cc_start: 0.7779 (t0) cc_final: 0.7284 (t70) REVERT: A 75 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7432 (mm-30) REVERT: A 80 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6795 (mm-30) REVERT: B 59 ASP cc_start: 0.7776 (t0) cc_final: 0.7275 (t70) REVERT: B 75 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7433 (mm-30) REVERT: B 80 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6795 (mm-30) REVERT: C 59 ASP cc_start: 0.7780 (t0) cc_final: 0.7289 (t70) REVERT: C 75 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7432 (mm-30) REVERT: C 80 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6796 (mm-30) REVERT: D 59 ASP cc_start: 0.7796 (t0) cc_final: 0.7320 (t70) REVERT: D 75 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7434 (mm-30) REVERT: D 80 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6802 (mm-30) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1727 time to fit residues: 14.1868 Evaluate side-chains 68 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4496 r_free = 0.4496 target = 0.231079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.203627 restraints weight = 3089.361| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 2.21 r_work: 0.4022 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3192 Z= 0.144 Angle : 0.479 6.562 4284 Z= 0.244 Chirality : 0.033 0.097 480 Planarity : 0.003 0.024 568 Dihedral : 3.407 11.695 440 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 17.24 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.32 (0.37), residues: 416 helix: 3.31 (0.23), residues: 360 sheet: None (None), residues: 0 loop : -0.63 (0.87), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 34 PHE 0.009 0.002 PHE B 23 TYR 0.004 0.001 TYR A 4 ARG 0.007 0.001 ARG D 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 942.39 seconds wall clock time: 19 minutes 12.08 seconds (1152.08 seconds total)