Starting phenix.real_space_refine on Sun Mar 10 15:11:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag3_15414/03_2024/8ag3_15414.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag3_15414/03_2024/8ag3_15414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag3_15414/03_2024/8ag3_15414.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag3_15414/03_2024/8ag3_15414.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag3_15414/03_2024/8ag3_15414.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag3_15414/03_2024/8ag3_15414.pdb" } resolution = 3.47 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= 0.015 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 20 5.16 5 C 1668 2.51 5 N 436 2.21 5 O 508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2632 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1316 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Chain: "D" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1316 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Time building chain proxies: 1.79, per 1000 atoms: 0.68 Number of scatterers: 2632 At special positions: 0 Unit cell: (78.49, 64.295, 64.295, 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 20 16.00 O 508 8.00 N 436 7.00 C 1668 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 457.5 milliseconds 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 16.1% alpha, 52.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'C' and resid 20 through 31 removed outlier: 3.778A pdb=" N ASN C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 60 Processing helix chain 'D' and resid 22 through 31 Processing helix chain 'D' and resid 46 through 61 removed outlier: 4.125A pdb=" N ILE D 50 " --> pdb=" O ASN D 46 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 38 through 42 removed outlier: 7.238A pdb=" N THR C 72 " --> pdb=" O ASP C 155 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASP C 155 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 149 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR C 150 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N THR C 11 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE D 3 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR D 11 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP D 130 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 103 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR D 150 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS D 149 " --> pdb=" O TYR D 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 64 through 69 removed outlier: 3.619A pdb=" N CYS C 66 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR C 150 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N THR C 11 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE D 3 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR D 11 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP D 130 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 103 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR D 150 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.897A pdb=" N PHE C 139 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP C 138 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C 127 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 112 through 113 removed outlier: 6.831A pdb=" N CYS D 112 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU D 145 " --> pdb=" O CYS D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 150 hydrogen bonds defined for protein. 423 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: 0.71 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 852 1.35 - 1.46: 557 1.46 - 1.58: 1237 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 2676 Sorted by residual: bond pdb=" CB GLU C 65 " pdb=" CG GLU C 65 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" CB PRO C 80 " pdb=" CG PRO C 80 " ideal model delta sigma weight residual 1.492 1.540 -0.048 5.00e-02 4.00e+02 9.38e-01 bond pdb=" CA GLU C 65 " pdb=" CB GLU C 65 " ideal model delta sigma weight residual 1.534 1.546 -0.013 1.45e-02 4.76e+03 7.44e-01 bond pdb=" CB MET D 43 " pdb=" CG MET D 43 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.20e-01 bond pdb=" CA LYS D 7 " pdb=" CB LYS D 7 " ideal model delta sigma weight residual 1.530 1.541 -0.011 1.68e-02 3.54e+03 4.56e-01 ... (remaining 2671 not shown) Histogram of bond angle deviations from ideal: 98.95 - 105.95: 42 105.95 - 112.94: 1478 112.94 - 119.94: 864 119.94 - 126.94: 1210 126.94 - 133.94: 16 Bond angle restraints: 3610 Sorted by residual: angle pdb=" CA GLU C 65 " pdb=" CB GLU C 65 " pdb=" CG GLU C 65 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CA MET D 43 " pdb=" CB MET D 43 " pdb=" CG MET D 43 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CB MET D 43 " pdb=" CG MET D 43 " pdb=" SD MET D 43 " ideal model delta sigma weight residual 112.70 121.58 -8.88 3.00e+00 1.11e-01 8.77e+00 angle pdb=" CA PRO C 80 " pdb=" N PRO C 80 " pdb=" CD PRO C 80 " ideal model delta sigma weight residual 112.00 108.65 3.35 1.40e+00 5.10e-01 5.73e+00 angle pdb=" C MET D 43 " pdb=" CA MET D 43 " pdb=" CB MET D 43 " ideal model delta sigma weight residual 110.19 114.05 -3.86 1.62e+00 3.81e-01 5.66e+00 ... (remaining 3605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.04: 1299 13.04 - 26.08: 225 26.08 - 39.11: 81 39.11 - 52.15: 37 52.15 - 65.19: 12 Dihedral angle restraints: 1654 sinusoidal: 694 harmonic: 960 Sorted by residual: dihedral pdb=" CA ASP C 128 " pdb=" CB ASP C 128 " pdb=" CG ASP C 128 " pdb=" OD1 ASP C 128 " ideal model delta sinusoidal sigma weight residual -30.00 -89.18 59.18 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP C 83 " pdb=" CB ASP C 83 " pdb=" CG ASP C 83 " pdb=" OD1 ASP C 83 " ideal model delta sinusoidal sigma weight residual -30.00 -87.13 57.13 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA LYS D 77 " pdb=" CB LYS D 77 " pdb=" CG LYS D 77 " pdb=" CD LYS D 77 " ideal model delta sinusoidal sigma weight residual 60.00 117.48 -57.48 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 1651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 238 0.028 - 0.057: 103 0.057 - 0.085: 37 0.085 - 0.113: 28 0.113 - 0.141: 6 Chirality restraints: 412 Sorted by residual: chirality pdb=" CA ILE C 73 " pdb=" N ILE C 73 " pdb=" C ILE C 73 " pdb=" CB ILE C 73 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE C 105 " pdb=" N ILE C 105 " pdb=" C ILE C 105 " pdb=" CB ILE C 105 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CB ILE D 39 " pdb=" CA ILE D 39 " pdb=" CG1 ILE D 39 " pdb=" CG2 ILE D 39 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 409 not shown) Planarity restraints: 458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 79 " -0.088 5.00e-02 4.00e+02 1.33e-01 2.81e+01 pdb=" N PRO C 80 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 120 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO C 121 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET D 43 " -0.005 2.00e-02 2.50e+03 9.79e-03 9.58e-01 pdb=" C MET D 43 " 0.017 2.00e-02 2.50e+03 pdb=" O MET D 43 " -0.007 2.00e-02 2.50e+03 pdb=" N GLU D 44 " -0.006 2.00e-02 2.50e+03 ... (remaining 455 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 59 2.69 - 3.25: 2329 3.25 - 3.80: 3801 3.80 - 4.35: 5021 4.35 - 4.90: 8610 Nonbonded interactions: 19820 Sorted by model distance: nonbonded pdb=" O ASP C 48 " pdb=" ND2 ASN C 52 " model vdw 2.143 2.520 nonbonded pdb=" O GLN C 10 " pdb=" OH TYR C 101 " model vdw 2.232 2.440 nonbonded pdb=" O GLN D 10 " pdb=" OH TYR D 101 " model vdw 2.294 2.440 nonbonded pdb=" N GLU C 44 " pdb=" OE1 GLU C 44 " model vdw 2.344 2.520 nonbonded pdb=" NH1 ARG D 23 " pdb=" O TYR D 106 " model vdw 2.350 2.520 ... (remaining 19815 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 '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: 1.290 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: 5.540 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.830 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 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 : 0.002 0.048 2676 Z= 0.167 Angle : 0.600 8.883 3610 Z= 0.322 Chirality : 0.044 0.141 412 Planarity : 0.007 0.133 458 Dihedral : 17.158 65.191 1030 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 34.74 % Favored : 65.26 % 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: -1.45 (0.47), residues: 318 helix: 2.05 (0.79), residues: 50 sheet: -0.29 (0.51), residues: 112 loop : -2.61 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 91 HIS 0.002 0.001 HIS C 32 PHE 0.010 0.001 PHE D 15 TYR 0.009 0.001 TYR D 4 ARG 0.001 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: D 106 TYR cc_start: 0.8501 (m-80) cc_final: 0.8225 (m-80) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1688 time to fit residues: 20.2639 Evaluate side-chains 105 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 0.0670 chunk 9 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2676 Z= 0.215 Angle : 0.546 5.736 3610 Z= 0.293 Chirality : 0.044 0.140 412 Planarity : 0.006 0.098 458 Dihedral : 4.469 12.429 350 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 1.95 % Allowed : 30.84 % Favored : 67.21 % 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: -1.27 (0.48), residues: 318 helix: 2.04 (0.80), residues: 50 sheet: 0.01 (0.54), residues: 102 loop : -2.46 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 91 HIS 0.003 0.001 HIS C 120 PHE 0.013 0.001 PHE C 133 TYR 0.011 0.002 TYR D 101 ARG 0.001 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 0.338 Fit side-chains REVERT: C 43 MET cc_start: 0.4352 (tpp) cc_final: 0.4089 (tpt) REVERT: C 52 ASN cc_start: 0.7767 (m-40) cc_final: 0.7536 (m110) REVERT: C 75 PHE cc_start: 0.8031 (m-80) cc_final: 0.7411 (m-80) REVERT: C 119 TYR cc_start: 0.8372 (m-80) cc_final: 0.8116 (m-80) REVERT: D 49 ILE cc_start: 0.8088 (mm) cc_final: 0.7885 (mt) REVERT: D 106 TYR cc_start: 0.8521 (m-80) cc_final: 0.8287 (m-80) REVERT: D 156 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7878 (mm) outliers start: 6 outliers final: 4 residues processed: 109 average time/residue: 0.1638 time to fit residues: 20.7840 Evaluate side-chains 113 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.0770 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2676 Z= 0.191 Angle : 0.512 4.784 3610 Z= 0.279 Chirality : 0.043 0.142 412 Planarity : 0.005 0.086 458 Dihedral : 4.405 11.718 350 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.22 % Allowed : 27.92 % Favored : 67.86 % 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: -1.21 (0.48), residues: 318 helix: 2.13 (0.80), residues: 50 sheet: 0.03 (0.53), residues: 102 loop : -2.43 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 91 HIS 0.002 0.001 HIS C 120 PHE 0.012 0.001 PHE C 133 TYR 0.009 0.001 TYR D 101 ARG 0.003 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: C 43 MET cc_start: 0.4282 (tpp) cc_final: 0.4056 (tpt) REVERT: C 75 PHE cc_start: 0.8024 (m-80) cc_final: 0.7407 (m-80) REVERT: C 119 TYR cc_start: 0.8390 (m-80) cc_final: 0.8074 (m-80) REVERT: D 49 ILE cc_start: 0.8058 (mm) cc_final: 0.7829 (mt) REVERT: D 156 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7908 (mm) outliers start: 13 outliers final: 8 residues processed: 113 average time/residue: 0.1472 time to fit residues: 19.6206 Evaluate side-chains 115 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2676 Z= 0.264 Angle : 0.543 4.571 3610 Z= 0.298 Chirality : 0.045 0.152 412 Planarity : 0.005 0.082 458 Dihedral : 4.616 11.916 350 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 5.19 % Allowed : 25.65 % Favored : 69.16 % 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: -1.28 (0.47), residues: 318 helix: 1.93 (0.78), residues: 50 sheet: 0.04 (0.52), residues: 102 loop : -2.45 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 91 HIS 0.003 0.001 HIS C 120 PHE 0.014 0.001 PHE C 133 TYR 0.011 0.002 TYR D 101 ARG 0.001 0.000 ARG D 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: C 75 PHE cc_start: 0.8012 (m-80) cc_final: 0.7410 (m-80) REVERT: C 119 TYR cc_start: 0.8375 (m-80) cc_final: 0.8132 (m-80) REVERT: C 140 LYS cc_start: 0.8035 (tttp) cc_final: 0.7660 (tttp) REVERT: D 138 ASP cc_start: 0.7349 (p0) cc_final: 0.7073 (p0) REVERT: D 156 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7979 (mm) outliers start: 16 outliers final: 14 residues processed: 116 average time/residue: 0.1671 time to fit residues: 22.4121 Evaluate side-chains 123 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 0.0870 chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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: 0.7072 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2676 Z= 0.256 Angle : 0.541 4.867 3610 Z= 0.294 Chirality : 0.044 0.142 412 Planarity : 0.005 0.080 458 Dihedral : 4.565 12.507 350 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 6.49 % Allowed : 26.62 % Favored : 66.88 % 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: -1.32 (0.47), residues: 318 helix: 1.86 (0.77), residues: 50 sheet: 0.03 (0.52), residues: 102 loop : -2.47 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 91 HIS 0.003 0.001 HIS C 120 PHE 0.014 0.001 PHE C 133 TYR 0.012 0.002 TYR D 101 ARG 0.004 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 65 GLU cc_start: 0.6589 (tm-30) cc_final: 0.6349 (tm-30) REVERT: C 75 PHE cc_start: 0.8013 (m-80) cc_final: 0.7354 (m-80) REVERT: C 119 TYR cc_start: 0.8359 (m-80) cc_final: 0.8134 (m-80) REVERT: C 140 LYS cc_start: 0.8022 (tttp) cc_final: 0.7451 (tttp) REVERT: D 156 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7930 (mm) outliers start: 20 outliers final: 16 residues processed: 115 average time/residue: 0.1611 time to fit residues: 21.5835 Evaluate side-chains 123 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7096 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 2676 Z= 0.366 Angle : 0.608 8.332 3610 Z= 0.327 Chirality : 0.046 0.170 412 Planarity : 0.005 0.081 458 Dihedral : 4.871 13.985 350 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 5.19 % Allowed : 27.60 % Favored : 67.21 % 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: -1.48 (0.47), residues: 318 helix: 1.60 (0.76), residues: 50 sheet: 0.03 (0.52), residues: 102 loop : -2.62 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP D 91 HIS 0.003 0.001 HIS C 120 PHE 0.019 0.002 PHE C 133 TYR 0.014 0.002 TYR D 101 ARG 0.004 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: C 65 GLU cc_start: 0.6611 (tm-30) cc_final: 0.6342 (tm-30) REVERT: C 75 PHE cc_start: 0.8007 (m-80) cc_final: 0.7392 (m-80) REVERT: C 119 TYR cc_start: 0.8375 (m-80) cc_final: 0.8142 (m-80) REVERT: C 140 LYS cc_start: 0.8026 (tttp) cc_final: 0.7464 (tttp) REVERT: D 138 ASP cc_start: 0.7313 (p0) cc_final: 0.7033 (p0) REVERT: D 156 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.8043 (mm) outliers start: 16 outliers final: 15 residues processed: 126 average time/residue: 0.1654 time to fit residues: 24.0336 Evaluate side-chains 136 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.0270 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- 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: 0.7060 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2676 Z= 0.201 Angle : 0.560 8.721 3610 Z= 0.292 Chirality : 0.045 0.147 412 Planarity : 0.005 0.078 458 Dihedral : 4.551 12.836 350 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 4.22 % Allowed : 30.52 % Favored : 65.26 % 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: -1.28 (0.47), residues: 318 helix: 1.91 (0.78), residues: 50 sheet: 0.12 (0.53), residues: 102 loop : -2.51 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 PHE 0.013 0.001 PHE C 133 TYR 0.010 0.001 TYR D 101 ARG 0.001 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: C 65 GLU cc_start: 0.6608 (tm-30) cc_final: 0.6306 (tm-30) REVERT: C 75 PHE cc_start: 0.8007 (m-80) cc_final: 0.7358 (m-80) REVERT: C 119 TYR cc_start: 0.8366 (m-80) cc_final: 0.8088 (m-80) REVERT: C 140 LYS cc_start: 0.8014 (tttp) cc_final: 0.7417 (tttp) REVERT: D 156 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8004 (mm) outliers start: 13 outliers final: 10 residues processed: 110 average time/residue: 0.1546 time to fit residues: 19.8329 Evaluate side-chains 117 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 24 optimal weight: 0.0770 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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: 0.7067 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2676 Z= 0.228 Angle : 0.578 8.964 3610 Z= 0.299 Chirality : 0.045 0.148 412 Planarity : 0.005 0.078 458 Dihedral : 4.574 12.914 350 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 4.55 % Allowed : 29.87 % Favored : 65.58 % 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: -1.26 (0.47), residues: 318 helix: 2.00 (0.79), residues: 50 sheet: 0.16 (0.53), residues: 102 loop : -2.55 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 PHE 0.014 0.001 PHE C 133 TYR 0.011 0.002 TYR D 101 ARG 0.001 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 65 GLU cc_start: 0.6614 (tm-30) cc_final: 0.6296 (tm-30) REVERT: C 75 PHE cc_start: 0.8000 (m-80) cc_final: 0.7357 (m-80) REVERT: C 119 TYR cc_start: 0.8364 (m-80) cc_final: 0.8083 (m-80) REVERT: C 140 LYS cc_start: 0.8038 (tttp) cc_final: 0.7458 (tttp) REVERT: D 138 ASP cc_start: 0.7290 (p0) cc_final: 0.7016 (p0) REVERT: D 156 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7995 (mm) outliers start: 14 outliers final: 12 residues processed: 112 average time/residue: 0.1736 time to fit residues: 22.4436 Evaluate side-chains 119 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 0.0870 chunk 28 optimal weight: 0.0770 chunk 18 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.0870 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 overall best weight: 0.3094 ------------------------------------------------------------------------------- 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: 0.7049 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2676 Z= 0.166 Angle : 0.549 9.811 3610 Z= 0.284 Chirality : 0.044 0.142 412 Planarity : 0.005 0.078 458 Dihedral : 4.377 12.854 350 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.22 % Allowed : 30.19 % Favored : 65.58 % 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: -1.13 (0.48), residues: 318 helix: 2.24 (0.80), residues: 50 sheet: 0.19 (0.53), residues: 102 loop : -2.47 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 PHE 0.012 0.001 PHE C 133 TYR 0.009 0.001 TYR D 101 ARG 0.007 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: C 65 GLU cc_start: 0.6606 (tm-30) cc_final: 0.6288 (tm-30) REVERT: C 75 PHE cc_start: 0.8012 (m-80) cc_final: 0.7317 (m-80) REVERT: C 119 TYR cc_start: 0.8350 (m-80) cc_final: 0.8040 (m-80) REVERT: C 140 LYS cc_start: 0.8023 (tttp) cc_final: 0.7408 (tttp) REVERT: D 156 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7962 (mm) outliers start: 13 outliers final: 12 residues processed: 111 average time/residue: 0.1615 time to fit residues: 20.8086 Evaluate side-chains 118 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 0.0570 chunk 10 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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: 0.7059 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2676 Z= 0.210 Angle : 0.568 10.369 3610 Z= 0.294 Chirality : 0.044 0.141 412 Planarity : 0.005 0.077 458 Dihedral : 4.457 12.907 350 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 4.22 % Allowed : 30.84 % Favored : 64.94 % 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: -1.14 (0.48), residues: 318 helix: 2.17 (0.79), residues: 50 sheet: 0.26 (0.54), residues: 102 loop : -2.51 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 PHE 0.014 0.001 PHE C 133 TYR 0.010 0.001 TYR D 101 ARG 0.005 0.000 ARG C 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: C 65 GLU cc_start: 0.6610 (tm-30) cc_final: 0.6291 (tm-30) REVERT: C 75 PHE cc_start: 0.8007 (m-80) cc_final: 0.7370 (m-80) REVERT: C 119 TYR cc_start: 0.8355 (m-80) cc_final: 0.8080 (m-80) REVERT: C 140 LYS cc_start: 0.8009 (tttp) cc_final: 0.7422 (tttp) REVERT: D 138 ASP cc_start: 0.7323 (p0) cc_final: 0.7025 (p0) REVERT: D 156 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7975 (mm) outliers start: 13 outliers final: 12 residues processed: 112 average time/residue: 0.1582 time to fit residues: 20.5316 Evaluate side-chains 119 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 1 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.131363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107695 restraints weight = 3720.975| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.55 r_work: 0.3168 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2676 Z= 0.223 Angle : 0.592 10.657 3610 Z= 0.300 Chirality : 0.045 0.168 412 Planarity : 0.005 0.078 458 Dihedral : 4.462 12.877 350 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 4.22 % Allowed : 31.49 % Favored : 64.29 % 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: -1.12 (0.48), residues: 318 helix: 2.14 (0.79), residues: 50 sheet: 0.29 (0.54), residues: 102 loop : -2.49 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 PHE 0.014 0.001 PHE C 133 TYR 0.011 0.001 TYR D 101 ARG 0.006 0.000 ARG C 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1270.56 seconds wall clock time: 23 minutes 14.71 seconds (1394.71 seconds total)