Starting phenix.real_space_refine on Tue Feb 13 06:29:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6j_0689/02_2024/6j6j_0689.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6j_0689/02_2024/6j6j_0689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6j_0689/02_2024/6j6j_0689.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6j_0689/02_2024/6j6j_0689.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6j_0689/02_2024/6j6j_0689.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j6j_0689/02_2024/6j6j_0689.pdb" } resolution = 3.2 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= 0.020 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 4 5.16 5 C 2264 2.51 5 N 628 2.21 5 O 728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 44": "OE1" <-> "OE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 44": "OE1" <-> "OE2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3624 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.53, per 1000 atoms: 0.70 Number of scatterers: 3624 At special positions: 0 Unit cell: (70.551, 60.021, 64.233, 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 4 16.00 O 728 8.00 N 628 7.00 C 2264 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: 1.30 Conformation dependent library (CDL) restraints added in 812.6 milliseconds 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 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: 0 helices and 4 sheets defined 0.0% alpha, 47.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 4.058A pdb=" N GLY A 41 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER A 88 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 21 removed outlier: 4.058A pdb=" N GLY B 41 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL B 55 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA B 78 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N SER B 88 " --> pdb=" O TRP B 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 19 through 21 removed outlier: 4.057A pdb=" N GLY C 41 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N VAL C 55 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA C 78 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER C 88 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 19 through 21 removed outlier: 4.059A pdb=" N GLY D 41 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL D 55 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA D 78 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER D 88 " --> pdb=" O TRP D 79 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 492 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: 0.91 Time building geometry restraints manager: 1.43 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: 1159 1.34 - 1.46: 1020 1.46 - 1.57: 1517 1.57 - 1.69: 4 1.69 - 1.81: 4 Bond restraints: 3704 Sorted by residual: bond pdb=" C3 BTN C5100 " pdb=" O3 BTN C5100 " ideal model delta sigma weight residual 1.220 1.405 -0.185 2.00e-02 2.50e+03 8.53e+01 bond pdb=" C3 BTN D5100 " pdb=" O3 BTN D5100 " ideal model delta sigma weight residual 1.220 1.404 -0.184 2.00e-02 2.50e+03 8.47e+01 bond pdb=" C3 BTN A5100 " pdb=" O3 BTN A5100 " ideal model delta sigma weight residual 1.220 1.403 -0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" C3 BTN B5100 " pdb=" O3 BTN B5100 " ideal model delta sigma weight residual 1.220 1.403 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" C2 BTN C5100 " pdb=" S1 BTN C5100 " ideal model delta sigma weight residual 1.824 1.663 0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 3699 not shown) Histogram of bond angle deviations from ideal: 90.85 - 99.50: 4 99.50 - 108.15: 199 108.15 - 116.81: 2479 116.81 - 125.46: 2270 125.46 - 134.11: 116 Bond angle restraints: 5068 Sorted by residual: angle pdb=" C SER B 62 " pdb=" N ALA B 63 " pdb=" CA ALA B 63 " ideal model delta sigma weight residual 121.80 130.14 -8.34 2.44e+00 1.68e-01 1.17e+01 angle pdb=" C SER A 62 " pdb=" N ALA A 63 " pdb=" CA ALA A 63 " ideal model delta sigma weight residual 121.80 130.12 -8.32 2.44e+00 1.68e-01 1.16e+01 angle pdb=" C SER C 62 " pdb=" N ALA C 63 " pdb=" CA ALA C 63 " ideal model delta sigma weight residual 121.80 130.10 -8.30 2.44e+00 1.68e-01 1.16e+01 angle pdb=" C SER D 62 " pdb=" N ALA D 63 " pdb=" CA ALA D 63 " ideal model delta sigma weight residual 121.80 130.03 -8.23 2.44e+00 1.68e-01 1.14e+01 angle pdb=" C GLU A 51 " pdb=" N SER A 52 " pdb=" CA SER A 52 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 ... (remaining 5063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.87: 1724 13.87 - 27.74: 276 27.74 - 41.60: 52 41.60 - 55.47: 8 55.47 - 69.34: 4 Dihedral angle restraints: 2064 sinusoidal: 744 harmonic: 1320 Sorted by residual: dihedral pdb=" CA ALA C 63 " pdb=" C ALA C 63 " pdb=" N PRO C 64 " pdb=" CA PRO C 64 " ideal model delta harmonic sigma weight residual -180.00 -154.75 -25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ALA D 63 " pdb=" C ALA D 63 " pdb=" N PRO D 64 " pdb=" CA PRO D 64 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ALA A 63 " pdb=" C ALA A 63 " pdb=" N PRO A 64 " pdb=" CA PRO A 64 " ideal model delta harmonic sigma weight residual 180.00 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 2061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 421 0.057 - 0.114: 99 0.114 - 0.172: 40 0.172 - 0.229: 4 0.229 - 0.286: 4 Chirality restraints: 568 Sorted by residual: chirality pdb=" C2 BTN C5100 " pdb=" C4 BTN C5100 " pdb=" C7 BTN C5100 " pdb=" S1 BTN C5100 " both_signs ideal model delta sigma weight residual False 3.08 2.80 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C2 BTN B5100 " pdb=" C4 BTN B5100 " pdb=" C7 BTN B5100 " pdb=" S1 BTN B5100 " both_signs ideal model delta sigma weight residual False 3.08 2.80 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C2 BTN D5100 " pdb=" C4 BTN D5100 " pdb=" C7 BTN D5100 " pdb=" S1 BTN D5100 " both_signs ideal model delta sigma weight residual False 3.08 2.80 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 565 not shown) Planarity restraints: 632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTN B5100 " 0.002 2.00e-02 2.50e+03 3.58e-02 1.93e+01 pdb=" C4 BTN B5100 " -0.055 2.00e-02 2.50e+03 pdb=" C5 BTN B5100 " 0.046 2.00e-02 2.50e+03 pdb=" N1 BTN B5100 " -0.028 2.00e-02 2.50e+03 pdb=" N2 BTN B5100 " 0.041 2.00e-02 2.50e+03 pdb=" O3 BTN B5100 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTN A5100 " 0.002 2.00e-02 2.50e+03 3.56e-02 1.90e+01 pdb=" C4 BTN A5100 " -0.054 2.00e-02 2.50e+03 pdb=" C5 BTN A5100 " 0.046 2.00e-02 2.50e+03 pdb=" N1 BTN A5100 " -0.028 2.00e-02 2.50e+03 pdb=" N2 BTN A5100 " 0.041 2.00e-02 2.50e+03 pdb=" O3 BTN A5100 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTN D5100 " -0.002 2.00e-02 2.50e+03 3.55e-02 1.90e+01 pdb=" C4 BTN D5100 " 0.054 2.00e-02 2.50e+03 pdb=" C5 BTN D5100 " -0.046 2.00e-02 2.50e+03 pdb=" N1 BTN D5100 " 0.029 2.00e-02 2.50e+03 pdb=" N2 BTN D5100 " -0.041 2.00e-02 2.50e+03 pdb=" O3 BTN D5100 " 0.006 2.00e-02 2.50e+03 ... (remaining 629 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1171 2.81 - 3.33: 2720 3.33 - 3.86: 6145 3.86 - 4.38: 6884 4.38 - 4.90: 12906 Nonbonded interactions: 29826 Sorted by model distance: nonbonded pdb=" OH TYR C 43 " pdb=" O3 BTN C5100 " model vdw 2.291 2.440 nonbonded pdb=" OH TYR D 43 " pdb=" O3 BTN D5100 " model vdw 2.291 2.440 nonbonded pdb=" OH TYR B 43 " pdb=" O3 BTN B5100 " model vdw 2.292 2.440 nonbonded pdb=" OH TYR A 43 " pdb=" O3 BTN A5100 " model vdw 2.292 2.440 nonbonded pdb=" ND2 ASN A 23 " pdb=" OG SER A 27 " model vdw 2.322 2.520 ... (remaining 29821 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: 0.070 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: 0.620 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 14.410 Find NCS groups from input model: 0.230 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 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 : 0.011 0.185 3704 Z= 0.686 Angle : 1.065 8.418 5068 Z= 0.564 Chirality : 0.061 0.286 568 Planarity : 0.005 0.036 632 Dihedral : 13.509 69.341 1240 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 19.77 % Favored : 80.23 % 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: -3.36 (0.33), residues: 468 helix: None (None), residues: 0 sheet: -1.47 (0.27), residues: 284 loop : -3.38 (0.35), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 75 HIS 0.002 0.001 HIS B 87 PHE 0.018 0.003 PHE A 29 TYR 0.016 0.002 TYR C 96 ARG 0.006 0.001 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.349 Fit side-chains REVERT: A 105 ASN cc_start: 0.8185 (m110) cc_final: 0.7865 (m110) REVERT: B 105 ASN cc_start: 0.7803 (m110) cc_final: 0.7563 (m-40) REVERT: D 83 TYR cc_start: 0.7863 (m-10) cc_final: 0.7403 (m-10) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1961 time to fit residues: 15.8345 Evaluate side-chains 54 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN B 81 ASN B 105 ASN B 107 GLN C 105 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3704 Z= 0.171 Angle : 0.594 7.195 5068 Z= 0.322 Chirality : 0.043 0.139 568 Planarity : 0.003 0.030 632 Dihedral : 6.196 30.869 592 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.36 % Allowed : 18.02 % Favored : 77.62 % 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: -2.46 (0.35), residues: 468 helix: None (None), residues: 0 sheet: -0.29 (0.32), residues: 220 loop : -3.06 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 92 HIS 0.001 0.001 HIS B 127 PHE 0.012 0.002 PHE C 29 TYR 0.009 0.001 TYR D 43 ARG 0.002 0.000 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 52 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 115 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.8007 (m) REVERT: B 56 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.7046 (pp) REVERT: C 56 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6884 (pp) REVERT: D 81 ASN cc_start: 0.7957 (p0) cc_final: 0.7636 (p0) outliers start: 15 outliers final: 4 residues processed: 67 average time/residue: 0.1645 time to fit residues: 13.5657 Evaluate side-chains 49 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 56 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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: 0.6895 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 3704 Z= 0.450 Angle : 0.799 7.349 5068 Z= 0.424 Chirality : 0.049 0.161 568 Planarity : 0.006 0.048 632 Dihedral : 7.311 32.553 592 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 6.40 % Allowed : 17.15 % Favored : 76.45 % 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: -2.85 (0.37), residues: 468 helix: None (None), residues: 0 sheet: -1.33 (0.28), residues: 284 loop : -2.66 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 75 HIS 0.006 0.003 HIS A 127 PHE 0.018 0.004 PHE C 29 TYR 0.019 0.003 TYR C 43 ARG 0.003 0.001 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 51 time to evaluate : 0.404 Fit side-chains outliers start: 22 outliers final: 15 residues processed: 66 average time/residue: 0.1388 time to fit residues: 11.7156 Evaluate side-chains 63 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 48 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 0.0980 chunk 30 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 38 optimal weight: 0.0060 chunk 11 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.8202 ------------------------------------------------------------------------------- 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: 0.6850 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3704 Z= 0.241 Angle : 0.638 7.319 5068 Z= 0.343 Chirality : 0.043 0.133 568 Planarity : 0.004 0.042 632 Dihedral : 6.349 29.938 592 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.07 % Allowed : 21.22 % Favored : 74.71 % 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: -2.70 (0.37), residues: 468 helix: None (None), residues: 0 sheet: -1.23 (0.27), residues: 284 loop : -2.57 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 75 HIS 0.003 0.001 HIS D 87 PHE 0.014 0.002 PHE C 29 TYR 0.009 0.002 TYR D 43 ARG 0.002 0.000 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.388 Fit side-chains REVERT: C 56 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6784 (pp) outliers start: 14 outliers final: 13 residues processed: 50 average time/residue: 0.1621 time to fit residues: 10.2654 Evaluate side-chains 55 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 41 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 118 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 0.2980 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- 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: 0.6910 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 3704 Z= 0.482 Angle : 0.787 7.336 5068 Z= 0.414 Chirality : 0.049 0.156 568 Planarity : 0.006 0.049 632 Dihedral : 7.257 30.796 592 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 8.14 % Allowed : 18.31 % Favored : 73.55 % 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: -2.85 (0.37), residues: 468 helix: None (None), residues: 0 sheet: -1.36 (0.27), residues: 284 loop : -2.60 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 75 HIS 0.005 0.003 HIS D 127 PHE 0.017 0.003 PHE C 29 TYR 0.017 0.003 TYR B 43 ARG 0.002 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 46 time to evaluate : 0.386 Fit side-chains outliers start: 28 outliers final: 24 residues processed: 68 average time/residue: 0.1343 time to fit residues: 11.7637 Evaluate side-chains 68 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 44 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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: 0.6882 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3704 Z= 0.315 Angle : 0.682 7.380 5068 Z= 0.361 Chirality : 0.045 0.137 568 Planarity : 0.005 0.043 632 Dihedral : 6.684 30.061 592 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 7.85 % Allowed : 19.48 % Favored : 72.67 % 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: -2.77 (0.37), residues: 468 helix: None (None), residues: 0 sheet: -1.29 (0.27), residues: 284 loop : -2.58 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 75 HIS 0.004 0.002 HIS D 87 PHE 0.015 0.003 PHE B 29 TYR 0.012 0.002 TYR A 43 ARG 0.001 0.000 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 44 time to evaluate : 0.403 Fit side-chains REVERT: D 53 ARG cc_start: 0.8367 (ttm170) cc_final: 0.8155 (ttm110) outliers start: 27 outliers final: 26 residues processed: 63 average time/residue: 0.1389 time to fit residues: 11.1957 Evaluate side-chains 67 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 41 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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: 0.6855 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3704 Z= 0.237 Angle : 0.620 7.093 5068 Z= 0.331 Chirality : 0.043 0.131 568 Planarity : 0.004 0.037 632 Dihedral : 6.272 29.126 592 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 6.69 % Allowed : 20.93 % Favored : 72.38 % 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: -2.62 (0.37), residues: 468 helix: None (None), residues: 0 sheet: -1.19 (0.27), residues: 288 loop : -2.50 (0.49), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 75 HIS 0.003 0.001 HIS D 87 PHE 0.014 0.002 PHE A 29 TYR 0.013 0.002 TYR C 60 ARG 0.002 0.000 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 42 time to evaluate : 0.387 Fit side-chains REVERT: B 107 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7441 (tp40) REVERT: D 53 ARG cc_start: 0.8163 (ttm170) cc_final: 0.7730 (ttm110) outliers start: 23 outliers final: 21 residues processed: 55 average time/residue: 0.1443 time to fit residues: 10.0356 Evaluate side-chains 63 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 41 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.0970 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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: 0.6837 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3704 Z= 0.201 Angle : 0.585 6.796 5068 Z= 0.315 Chirality : 0.042 0.129 568 Planarity : 0.004 0.038 632 Dihedral : 5.936 28.955 592 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 6.69 % Allowed : 22.67 % Favored : 70.64 % 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: -2.50 (0.37), residues: 468 helix: None (None), residues: 0 sheet: -1.18 (0.27), residues: 296 loop : -2.33 (0.50), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 75 HIS 0.003 0.001 HIS D 87 PHE 0.013 0.002 PHE A 29 TYR 0.010 0.001 TYR C 60 ARG 0.002 0.000 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 45 time to evaluate : 0.395 Fit side-chains REVERT: A 49 ASN cc_start: 0.7343 (t0) cc_final: 0.7135 (t0) REVERT: B 107 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7348 (tp40) outliers start: 23 outliers final: 22 residues processed: 58 average time/residue: 0.1572 time to fit residues: 11.6755 Evaluate side-chains 66 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 43 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 0.0470 chunk 41 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- 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: 0.6891 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 3704 Z= 0.372 Angle : 0.698 6.560 5068 Z= 0.369 Chirality : 0.046 0.139 568 Planarity : 0.005 0.039 632 Dihedral : 6.702 30.892 592 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 9.01 % Allowed : 21.22 % Favored : 69.77 % 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: -2.49 (0.37), residues: 468 helix: None (None), residues: 0 sheet: -1.06 (0.27), residues: 284 loop : -2.50 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 75 HIS 0.004 0.002 HIS D 87 PHE 0.015 0.003 PHE B 29 TYR 0.013 0.002 TYR C 60 ARG 0.002 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 42 time to evaluate : 0.352 Fit side-chains REVERT: B 107 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7482 (tp40) REVERT: D 53 ARG cc_start: 0.8287 (ttm170) cc_final: 0.8084 (ttp-170) outliers start: 31 outliers final: 27 residues processed: 63 average time/residue: 0.1376 time to fit residues: 11.0542 Evaluate side-chains 69 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 41 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.6851 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3704 Z= 0.229 Angle : 0.603 6.229 5068 Z= 0.326 Chirality : 0.043 0.130 568 Planarity : 0.004 0.037 632 Dihedral : 6.046 29.386 592 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 7.27 % Allowed : 22.38 % Favored : 70.35 % 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: -2.45 (0.37), residues: 468 helix: None (None), residues: 0 sheet: -1.07 (0.27), residues: 288 loop : -2.41 (0.49), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 75 HIS 0.003 0.001 HIS D 87 PHE 0.013 0.002 PHE A 29 TYR 0.017 0.002 TYR D 60 ARG 0.002 0.000 ARG D 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 43 time to evaluate : 0.402 Fit side-chains REVERT: B 62 SER cc_start: 0.7080 (m) cc_final: 0.6544 (p) REVERT: B 107 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7436 (tp40) outliers start: 25 outliers final: 24 residues processed: 57 average time/residue: 0.1504 time to fit residues: 11.0092 Evaluate side-chains 68 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 43 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.169879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.154888 restraints weight = 4010.302| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.81 r_work: 0.3713 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3704 Z= 0.291 Angle : 0.635 6.220 5068 Z= 0.341 Chirality : 0.044 0.134 568 Planarity : 0.004 0.036 632 Dihedral : 6.326 30.286 592 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 8.14 % Allowed : 21.80 % Favored : 70.06 % 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: -2.51 (0.37), residues: 468 helix: None (None), residues: 0 sheet: -1.13 (0.27), residues: 288 loop : -2.40 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 75 HIS 0.004 0.002 HIS D 87 PHE 0.014 0.002 PHE B 29 TYR 0.013 0.002 TYR D 60 ARG 0.002 0.000 ARG D 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1087.05 seconds wall clock time: 20 minutes 27.92 seconds (1227.92 seconds total)