Starting phenix.real_space_refine on Thu Nov 14 02:13:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9n_34574/11_2024/8h9n_34574.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9n_34574/11_2024/8h9n_34574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9n_34574/11_2024/8h9n_34574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9n_34574/11_2024/8h9n_34574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9n_34574/11_2024/8h9n_34574.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9n_34574/11_2024/8h9n_34574.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 11 5.16 5 C 2176 2.51 5 N 560 2.21 5 O 634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 3 Chain: "K" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1573 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 62} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1259 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 144} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 5.25, per 1000 atoms: 1.55 Number of scatterers: 3381 At special positions: 0 Unit cell: (81.03, 96.36, 207.32, 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 11 16.00 O 634 8.00 N 560 7.00 C 2176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 402.9 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 814 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 1 sheets defined 72.7% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'K' and resid 19 through 30 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 32 through 48 Processing helix chain 'K' and resid 54 through 121 removed outlier: 3.900A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix Processing helix chain 'K' and resid 122 through 182 Processing helix chain 'K' and resid 194 through 206 removed outlier: 3.789A pdb=" N LEU K 201 " --> pdb=" O CYS K 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 55 Processing helix chain 'L' and resid 67 through 83 removed outlier: 4.318A pdb=" N ARG L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 18 removed outlier: 3.690A pdb=" N ILE M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 43 Processing helix chain 'M' and resid 53 through 58 Processing helix chain 'M' and resid 64 through 75 Processing helix chain 'M' and resid 85 through 123 removed outlier: 3.896A pdb=" N VAL M 89 " --> pdb=" O TYR M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 130 removed outlier: 3.690A pdb=" N MET M 130 " --> pdb=" O PHE M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 140 through 143 removed outlier: 3.662A pdb=" N LYS M 143 " --> pdb=" O PRO M 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 140 through 143' Processing sheet with id=AA1, first strand: chain 'K' and resid 12 through 13 237 hydrogen bonds defined for protein. 705 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: 0.80 Time building geometry restraints manager: 1.00 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: 1078 1.34 - 1.45: 470 1.45 - 1.57: 1887 1.57 - 1.69: 0 1.69 - 1.80: 21 Bond restraints: 3456 Sorted by residual: bond pdb=" N LEU M 76 " pdb=" CA LEU M 76 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.25e-02 6.40e+03 6.36e+00 bond pdb=" N GLU K 178 " pdb=" CA GLU K 178 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.19e+00 bond pdb=" N LYS K 168 " pdb=" CA LYS K 168 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.89e+00 bond pdb=" CB PRO M 153 " pdb=" CG PRO M 153 " ideal model delta sigma weight residual 1.506 1.441 0.065 3.90e-02 6.57e+02 2.79e+00 bond pdb=" CB THR K 139 " pdb=" CG2 THR K 139 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.88e+00 ... (remaining 3451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 4467 1.92 - 3.84: 185 3.84 - 5.77: 19 5.77 - 7.69: 2 7.69 - 9.61: 1 Bond angle restraints: 4674 Sorted by residual: angle pdb=" C PHE K 125 " pdb=" N ASP K 126 " pdb=" CA ASP K 126 " ideal model delta sigma weight residual 120.31 114.62 5.69 1.52e+00 4.33e-01 1.40e+01 angle pdb=" C LYS K 72 " pdb=" N LYS K 73 " pdb=" CA LYS K 73 " ideal model delta sigma weight residual 121.80 114.95 6.85 2.16e+00 2.14e-01 1.01e+01 angle pdb=" N ARG K 121 " pdb=" CA ARG K 121 " pdb=" C ARG K 121 " ideal model delta sigma weight residual 111.75 115.44 -3.69 1.28e+00 6.10e-01 8.31e+00 angle pdb=" C ILE K 174 " pdb=" N ASN K 175 " pdb=" CA ASN K 175 " ideal model delta sigma weight residual 120.68 115.80 4.88 1.70e+00 3.46e-01 8.24e+00 angle pdb=" CA LEU K 117 " pdb=" CB LEU K 117 " pdb=" CG LEU K 117 " ideal model delta sigma weight residual 116.30 125.91 -9.61 3.50e+00 8.16e-02 7.54e+00 ... (remaining 4669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 1847 16.70 - 33.39: 210 33.39 - 50.09: 40 50.09 - 66.79: 12 66.79 - 83.49: 4 Dihedral angle restraints: 2113 sinusoidal: 862 harmonic: 1251 Sorted by residual: dihedral pdb=" CA PHE L 100 " pdb=" C PHE L 100 " pdb=" N GLU L 101 " pdb=" CA GLU L 101 " ideal model delta harmonic sigma weight residual -180.00 -161.42 -18.58 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ILE M 10 " pdb=" C ILE M 10 " pdb=" N ASP M 11 " pdb=" CA ASP M 11 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ARG K 121 " pdb=" C ARG K 121 " pdb=" N HIS K 122 " pdb=" CA HIS K 122 " ideal model delta harmonic sigma weight residual -180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 220 0.029 - 0.058: 170 0.058 - 0.087: 67 0.087 - 0.116: 31 0.116 - 0.145: 20 Chirality restraints: 508 Sorted by residual: chirality pdb=" CA VAL M 80 " pdb=" N VAL M 80 " pdb=" C VAL M 80 " pdb=" CB VAL M 80 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA PHE K 58 " pdb=" N PHE K 58 " pdb=" C PHE K 58 " pdb=" CB PHE K 58 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA PRO K 76 " pdb=" N PRO K 76 " pdb=" C PRO K 76 " pdb=" CB PRO K 76 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 505 not shown) Planarity restraints: 603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE M 69 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C PHE M 69 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE M 69 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU M 70 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 159 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C ILE K 159 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE K 159 " -0.011 2.00e-02 2.50e+03 pdb=" N SER K 160 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE M 139 " 0.014 2.00e-02 2.50e+03 1.29e-02 2.90e+00 pdb=" CG PHE M 139 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE M 139 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE M 139 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE M 139 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE M 139 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE M 139 " 0.002 2.00e-02 2.50e+03 ... (remaining 600 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 295 2.72 - 3.27: 3535 3.27 - 3.81: 5368 3.81 - 4.36: 5909 4.36 - 4.90: 10125 Nonbonded interactions: 25232 Sorted by model distance: nonbonded pdb=" O VAL K 181 " pdb=" OG SER K 184 " model vdw 2.178 3.040 nonbonded pdb=" NZ LYS K 84 " pdb=" OE1 GLU K 87 " model vdw 2.254 3.120 nonbonded pdb=" NH1 ARG K 154 " pdb=" O THR L 89 " model vdw 2.272 3.120 nonbonded pdb=" OG1 THR L 56 " pdb=" O GLY L 59 " model vdw 2.274 3.040 nonbonded pdb=" OD1 ASP K 126 " pdb=" NH2 ARG K 129 " model vdw 2.278 3.120 ... (remaining 25227 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 6.590 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.150 Find NCS groups from input model: 0.030 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.007 0.065 3456 Z= 0.443 Angle : 0.878 9.610 4674 Z= 0.496 Chirality : 0.052 0.145 508 Planarity : 0.006 0.040 603 Dihedral : 15.253 83.485 1299 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.28 (0.34), residues: 413 helix: -1.09 (0.25), residues: 285 sheet: None (None), residues: 0 loop : -2.19 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP K 176 HIS 0.006 0.003 HIS K 158 PHE 0.030 0.003 PHE M 139 TYR 0.020 0.003 TYR K 140 ARG 0.004 0.001 ARG M 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 56 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7139 (tt0) REVERT: K 154 ARG cc_start: 0.7546 (mtt-85) cc_final: 0.7256 (mtp180) REVERT: K 169 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8248 (tp30) REVERT: L 47 ILE cc_start: 0.8384 (pt) cc_final: 0.7695 (pt) REVERT: L 91 PRO cc_start: 0.7630 (Cg_endo) cc_final: 0.7350 (Cg_exo) REVERT: L 103 ILE cc_start: 0.5678 (mt) cc_final: 0.5461 (mt) REVERT: L 105 LYS cc_start: 0.5593 (tmtt) cc_final: 0.5125 (tptt) REVERT: M 96 ASP cc_start: 0.8088 (t0) cc_final: 0.7866 (t70) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2306 time to fit residues: 30.8521 Evaluate side-chains 75 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 88 GLN K 98 GLN K 103 HIS K 115 GLN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 GLN M 23 GLN M 47 ASN M 59 ASN M 136 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3456 Z= 0.256 Angle : 0.640 7.541 4674 Z= 0.347 Chirality : 0.042 0.147 508 Planarity : 0.006 0.047 603 Dihedral : 5.160 45.435 452 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.23 % Allowed : 14.93 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.41), residues: 413 helix: 1.15 (0.30), residues: 286 sheet: None (None), residues: 0 loop : -1.79 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 53 HIS 0.004 0.002 HIS K 158 PHE 0.018 0.002 PHE L 93 TYR 0.019 0.002 TYR M 56 ARG 0.006 0.001 ARG M 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: K 154 ARG cc_start: 0.7459 (mtt-85) cc_final: 0.6963 (ttm170) REVERT: L 47 ILE cc_start: 0.8251 (pt) cc_final: 0.7714 (pt) REVERT: L 103 ILE cc_start: 0.5752 (mt) cc_final: 0.5345 (mt) REVERT: M 96 ASP cc_start: 0.7981 (t0) cc_final: 0.7735 (t70) REVERT: M 119 GLU cc_start: 0.6675 (tp30) cc_final: 0.6434 (tp30) outliers start: 15 outliers final: 10 residues processed: 94 average time/residue: 0.1964 time to fit residues: 21.6767 Evaluate side-chains 83 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 93 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 0.0770 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 0.0370 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 128 GLN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3456 Z= 0.170 Angle : 0.572 7.153 4674 Z= 0.307 Chirality : 0.039 0.140 508 Planarity : 0.005 0.042 603 Dihedral : 4.722 38.292 452 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.94 % Allowed : 18.59 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.53 (0.43), residues: 413 helix: 2.04 (0.31), residues: 285 sheet: None (None), residues: 0 loop : -1.44 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 53 HIS 0.002 0.001 HIS K 158 PHE 0.022 0.002 PHE K 24 TYR 0.018 0.002 TYR K 74 ARG 0.006 0.001 ARG M 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: K 169 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8305 (tp30) REVERT: K 178 GLU cc_start: 0.8085 (mm-30) cc_final: 0.6904 (tm-30) REVERT: L 47 ILE cc_start: 0.8259 (pt) cc_final: 0.7755 (pt) REVERT: M 92 GLU cc_start: 0.6890 (tp30) cc_final: 0.6561 (tp30) REVERT: M 96 ASP cc_start: 0.7992 (t0) cc_final: 0.7697 (t70) REVERT: M 119 GLU cc_start: 0.6710 (tp30) cc_final: 0.6493 (tp30) outliers start: 14 outliers final: 7 residues processed: 91 average time/residue: 0.1810 time to fit residues: 19.4146 Evaluate side-chains 78 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 169 GLU Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 93 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.0570 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS M 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3456 Z= 0.230 Angle : 0.595 5.342 4674 Z= 0.325 Chirality : 0.041 0.192 508 Planarity : 0.005 0.044 603 Dihedral : 4.532 29.681 452 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.23 % Allowed : 20.00 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.74 (0.43), residues: 413 helix: 2.19 (0.30), residues: 286 sheet: None (None), residues: 0 loop : -1.36 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 53 HIS 0.003 0.001 HIS K 180 PHE 0.026 0.002 PHE K 24 TYR 0.012 0.002 TYR M 85 ARG 0.006 0.001 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.413 Fit side-chains REVERT: K 165 MET cc_start: 0.8269 (mtp) cc_final: 0.6920 (tmm) REVERT: K 178 GLU cc_start: 0.8094 (mm-30) cc_final: 0.6937 (tm-30) REVERT: L 47 ILE cc_start: 0.8229 (pt) cc_final: 0.7809 (pt) REVERT: L 48 ARG cc_start: 0.8326 (tmt170) cc_final: 0.8048 (tmt170) REVERT: L 81 MET cc_start: 0.8075 (ppp) cc_final: 0.7834 (ppp) REVERT: M 92 GLU cc_start: 0.7060 (tp30) cc_final: 0.6727 (tp30) REVERT: M 96 ASP cc_start: 0.7965 (t0) cc_final: 0.7672 (t70) REVERT: M 119 GLU cc_start: 0.6785 (tp30) cc_final: 0.6505 (tp30) outliers start: 15 outliers final: 14 residues processed: 81 average time/residue: 0.1938 time to fit residues: 18.5134 Evaluate side-chains 80 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 180 HIS Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 93 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 0.0060 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3456 Z= 0.161 Angle : 0.565 7.616 4674 Z= 0.306 Chirality : 0.040 0.174 508 Planarity : 0.005 0.041 603 Dihedral : 4.349 24.915 452 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.23 % Allowed : 20.00 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.12 (0.42), residues: 413 helix: 2.49 (0.30), residues: 280 sheet: None (None), residues: 0 loop : -1.06 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 176 HIS 0.004 0.001 HIS K 180 PHE 0.019 0.002 PHE K 24 TYR 0.025 0.001 TYR M 85 ARG 0.004 0.001 ARG K 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.379 Fit side-chains REVERT: K 154 ARG cc_start: 0.7058 (mtp180) cc_final: 0.6538 (mtt180) REVERT: K 165 MET cc_start: 0.8264 (mtp) cc_final: 0.6935 (tmm) REVERT: L 47 ILE cc_start: 0.8227 (pt) cc_final: 0.7819 (pt) REVERT: M 92 GLU cc_start: 0.7047 (tp30) cc_final: 0.6705 (tp30) REVERT: M 96 ASP cc_start: 0.7945 (t0) cc_final: 0.7647 (t70) REVERT: M 119 GLU cc_start: 0.6803 (tp30) cc_final: 0.6518 (tp30) REVERT: M 157 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7107 (mp) outliers start: 15 outliers final: 13 residues processed: 79 average time/residue: 0.1898 time to fit residues: 17.7167 Evaluate side-chains 79 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 180 HIS Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 157 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3456 Z= 0.177 Angle : 0.595 7.666 4674 Z= 0.317 Chirality : 0.040 0.160 508 Planarity : 0.005 0.041 603 Dihedral : 4.248 19.592 452 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.51 % Allowed : 20.56 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.23 (0.42), residues: 413 helix: 2.59 (0.30), residues: 279 sheet: None (None), residues: 0 loop : -1.03 (0.55), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 33 HIS 0.002 0.001 HIS K 180 PHE 0.010 0.001 PHE L 100 TYR 0.024 0.002 TYR M 85 ARG 0.005 0.001 ARG L 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 154 ARG cc_start: 0.7055 (mtp180) cc_final: 0.6796 (mtt180) REVERT: K 165 MET cc_start: 0.8265 (mtp) cc_final: 0.6982 (tmm) REVERT: L 47 ILE cc_start: 0.8229 (pt) cc_final: 0.7882 (pt) REVERT: L 101 GLU cc_start: 0.5612 (mp0) cc_final: 0.5345 (mp0) REVERT: M 92 GLU cc_start: 0.7005 (tp30) cc_final: 0.6652 (tp30) REVERT: M 96 ASP cc_start: 0.7954 (t0) cc_final: 0.7683 (t70) REVERT: M 119 GLU cc_start: 0.6846 (tp30) cc_final: 0.6587 (tp30) REVERT: M 157 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7132 (mp) outliers start: 16 outliers final: 11 residues processed: 78 average time/residue: 0.2016 time to fit residues: 18.5448 Evaluate side-chains 77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 157 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.0010 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 17 optimal weight: 0.1980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3456 Z= 0.168 Angle : 0.603 6.990 4674 Z= 0.321 Chirality : 0.040 0.156 508 Planarity : 0.005 0.039 603 Dihedral : 4.131 19.685 452 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.66 % Allowed : 21.13 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.42), residues: 413 helix: 2.73 (0.30), residues: 280 sheet: None (None), residues: 0 loop : -0.90 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 176 HIS 0.002 0.000 HIS K 180 PHE 0.023 0.002 PHE K 24 TYR 0.022 0.001 TYR M 85 ARG 0.004 0.001 ARG K 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.468 Fit side-chains REVERT: K 120 LYS cc_start: 0.8624 (tppt) cc_final: 0.7920 (ttpt) REVERT: K 154 ARG cc_start: 0.6999 (mtp180) cc_final: 0.6671 (mtt180) REVERT: K 164 MET cc_start: 0.7246 (tpp) cc_final: 0.5595 (tpp) REVERT: L 47 ILE cc_start: 0.8219 (pt) cc_final: 0.7938 (pt) REVERT: L 55 GLN cc_start: 0.7861 (pp30) cc_final: 0.7594 (pp30) REVERT: L 74 GLU cc_start: 0.6662 (tt0) cc_final: 0.6270 (tt0) REVERT: M 92 GLU cc_start: 0.6987 (tp30) cc_final: 0.6594 (tp30) REVERT: M 119 GLU cc_start: 0.6898 (tp30) cc_final: 0.6632 (tp30) REVERT: M 157 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7111 (mp) outliers start: 13 outliers final: 8 residues processed: 81 average time/residue: 0.2343 time to fit residues: 22.3471 Evaluate side-chains 75 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 157 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 128 GLN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3456 Z= 0.259 Angle : 0.664 8.759 4674 Z= 0.356 Chirality : 0.042 0.139 508 Planarity : 0.005 0.047 603 Dihedral : 4.185 20.062 452 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.66 % Allowed : 21.41 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.24 (0.41), residues: 413 helix: 2.54 (0.30), residues: 280 sheet: None (None), residues: 0 loop : -0.90 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 176 HIS 0.003 0.001 HIS K 172 PHE 0.022 0.002 PHE K 125 TYR 0.024 0.002 TYR M 85 ARG 0.004 0.001 ARG K 167 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.398 Fit side-chains REVERT: K 120 LYS cc_start: 0.8639 (tppt) cc_final: 0.7880 (ttpt) REVERT: K 165 MET cc_start: 0.8338 (mtp) cc_final: 0.7011 (tmm) REVERT: M 92 GLU cc_start: 0.6957 (tp30) cc_final: 0.6615 (tp30) REVERT: M 119 GLU cc_start: 0.6957 (tp30) cc_final: 0.6664 (tp30) REVERT: M 157 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7179 (mp) outliers start: 13 outliers final: 10 residues processed: 78 average time/residue: 0.1732 time to fit residues: 16.0960 Evaluate side-chains 77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 180 HIS Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 157 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 130 ASN K 180 HIS ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3456 Z= 0.196 Angle : 0.665 7.582 4674 Z= 0.349 Chirality : 0.041 0.140 508 Planarity : 0.005 0.040 603 Dihedral : 4.163 19.991 452 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.54 % Allowed : 23.10 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.36 (0.42), residues: 413 helix: 2.59 (0.30), residues: 281 sheet: None (None), residues: 0 loop : -0.79 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 176 HIS 0.004 0.001 HIS K 180 PHE 0.027 0.002 PHE K 125 TYR 0.024 0.002 TYR M 85 ARG 0.008 0.001 ARG K 167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: K 120 LYS cc_start: 0.8659 (tppt) cc_final: 0.7916 (ttpt) REVERT: K 165 MET cc_start: 0.8267 (mtp) cc_final: 0.6952 (tmm) REVERT: L 55 GLN cc_start: 0.7944 (pp30) cc_final: 0.7676 (pp30) REVERT: M 92 GLU cc_start: 0.6895 (tp30) cc_final: 0.6527 (tp30) REVERT: M 119 GLU cc_start: 0.6922 (tp30) cc_final: 0.6620 (tp30) REVERT: M 157 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7127 (mp) outliers start: 9 outliers final: 8 residues processed: 71 average time/residue: 0.1849 time to fit residues: 15.4894 Evaluate side-chains 74 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 180 HIS Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 157 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.0070 chunk 4 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 180 HIS ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3456 Z= 0.192 Angle : 0.668 8.473 4674 Z= 0.351 Chirality : 0.042 0.194 508 Planarity : 0.005 0.040 603 Dihedral : 4.129 19.309 452 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.97 % Allowed : 23.94 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.42), residues: 413 helix: 2.65 (0.29), residues: 286 sheet: None (None), residues: 0 loop : -0.79 (0.58), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 176 HIS 0.002 0.000 HIS K 180 PHE 0.010 0.001 PHE K 125 TYR 0.024 0.001 TYR M 85 ARG 0.008 0.001 ARG K 167 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: K 120 LYS cc_start: 0.8661 (tppt) cc_final: 0.7939 (ttpt) REVERT: K 148 TYR cc_start: 0.7414 (t80) cc_final: 0.7204 (t80) REVERT: K 165 MET cc_start: 0.8196 (mtp) cc_final: 0.6892 (tmm) REVERT: L 50 TYR cc_start: 0.3142 (t80) cc_final: 0.2141 (t80) REVERT: L 55 GLN cc_start: 0.7909 (pp30) cc_final: 0.7638 (pp30) REVERT: M 92 GLU cc_start: 0.6794 (tp30) cc_final: 0.6425 (tp30) REVERT: M 119 GLU cc_start: 0.6872 (tp30) cc_final: 0.6562 (tp30) REVERT: M 157 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7102 (mp) outliers start: 7 outliers final: 6 residues processed: 69 average time/residue: 0.2001 time to fit residues: 16.2677 Evaluate side-chains 72 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 180 HIS Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 157 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 180 HIS ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.138472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.120493 restraints weight = 8165.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.120746 restraints weight = 4671.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.121285 restraints weight = 3726.946| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3456 Z= 0.197 Angle : 0.660 7.845 4674 Z= 0.347 Chirality : 0.042 0.190 508 Planarity : 0.005 0.040 603 Dihedral : 4.098 19.578 452 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.82 % Allowed : 23.38 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.42 (0.42), residues: 413 helix: 2.62 (0.30), residues: 281 sheet: None (None), residues: 0 loop : -0.72 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 176 HIS 0.002 0.001 HIS K 180 PHE 0.022 0.001 PHE K 24 TYR 0.023 0.001 TYR M 85 ARG 0.005 0.001 ARG K 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1475.97 seconds wall clock time: 27 minutes 19.77 seconds (1639.77 seconds total)