Starting phenix.real_space_refine on Thu Nov 14 02:23:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9r_34578/11_2024/8h9r_34578.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9r_34578/11_2024/8h9r_34578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9r_34578/11_2024/8h9r_34578.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9r_34578/11_2024/8h9r_34578.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9r_34578/11_2024/8h9r_34578.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9r_34578/11_2024/8h9r_34578.cif" } resolution = 3.97 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= 0.009 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 21 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: 5.12, per 1000 atoms: 1.51 Number of scatterers: 3381 At special positions: 0 Unit cell: (91.98, 94.9, 206.59, 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: 1.04 Conformation dependent library (CDL) restraints added in 410.1 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: 18 helices and 1 sheets defined 74.6% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'K' and resid 19 through 26 Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing helix chain 'K' and resid 32 through 48 removed outlier: 3.559A pdb=" N VAL K 36 " --> pdb=" O THR K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 121 removed outlier: 3.792A 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 removed outlier: 3.782A pdb=" N VAL K 182 " --> pdb=" O GLU K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 206 Processing helix chain 'L' and resid 41 through 55 Processing helix chain 'L' and resid 67 through 83 removed outlier: 4.303A pdb=" N ARG L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 18 removed outlier: 3.768A pdb=" N ILE M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 22 removed outlier: 5.643A pdb=" N ASN M 22 " --> pdb=" O ILE M 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 19 through 22' 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: 3.753A pdb=" N VAL M 89 " --> pdb=" O TYR M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 130 Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 140 through 143 Processing helix chain 'M' and resid 156 through 160 Processing sheet with id=AA1, first strand: chain 'K' and resid 12 through 13 239 hydrogen bonds defined for protein. 699 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: 0.79 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1089 1.34 - 1.46: 745 1.46 - 1.58: 1601 1.58 - 1.69: 0 1.69 - 1.81: 21 Bond restraints: 3456 Sorted by residual: bond pdb=" N ASP L 97 " pdb=" CA ASP L 97 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.64e+01 bond pdb=" N ARG L 48 " pdb=" CA ARG L 48 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.22e+00 bond pdb=" N ASN M 136 " pdb=" CA ASN M 136 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.17e-02 7.31e+03 5.67e+00 bond pdb=" CA LYS M 146 " pdb=" C LYS M 146 " ideal model delta sigma weight residual 1.522 1.490 0.032 1.38e-02 5.25e+03 5.36e+00 bond pdb=" N THR M 131 " pdb=" CA THR M 131 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.34e-02 5.57e+03 5.17e+00 ... (remaining 3451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 4469 1.73 - 3.46: 179 3.46 - 5.19: 22 5.19 - 6.92: 2 6.92 - 8.65: 2 Bond angle restraints: 4674 Sorted by residual: angle pdb=" N MET L 81 " pdb=" CA MET L 81 " pdb=" C MET L 81 " ideal model delta sigma weight residual 113.55 104.90 8.65 1.26e+00 6.30e-01 4.71e+01 angle pdb=" C PHE K 125 " pdb=" N ASP K 126 " pdb=" CA ASP K 126 " ideal model delta sigma weight residual 120.31 115.19 5.12 1.52e+00 4.33e-01 1.13e+01 angle pdb=" CA THR M 131 " pdb=" C THR M 131 " pdb=" O THR M 131 " ideal model delta sigma weight residual 121.87 118.12 3.75 1.16e+00 7.43e-01 1.05e+01 angle pdb=" N LYS K 152 " pdb=" CA LYS K 152 " pdb=" C LYS K 152 " ideal model delta sigma weight residual 111.28 108.29 2.99 1.09e+00 8.42e-01 7.52e+00 angle pdb=" CA ARG L 48 " pdb=" C ARG L 48 " pdb=" O ARG L 48 " ideal model delta sigma weight residual 120.82 118.04 2.78 1.05e+00 9.07e-01 7.02e+00 ... (remaining 4669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 1850 16.75 - 33.49: 202 33.49 - 50.24: 46 50.24 - 66.99: 10 66.99 - 83.73: 5 Dihedral angle restraints: 2113 sinusoidal: 862 harmonic: 1251 Sorted by residual: 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 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA PHE L 93 " pdb=" C PHE L 93 " pdb=" N LYS L 94 " pdb=" CA LYS L 94 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+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 -160.49 -19.51 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 2110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 350 0.045 - 0.090: 127 0.090 - 0.134: 28 0.134 - 0.179: 2 0.179 - 0.224: 1 Chirality restraints: 508 Sorted by residual: chirality pdb=" CA MET L 81 " pdb=" N MET L 81 " pdb=" C MET L 81 " pdb=" CB MET L 81 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE M 125 " pdb=" N ILE M 125 " pdb=" C ILE M 125 " pdb=" CB ILE M 125 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA LYS K 152 " pdb=" N LYS K 152 " pdb=" C LYS K 152 " pdb=" CB LYS K 152 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 505 not shown) Planarity restraints: 603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU L 96 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.92e+00 pdb=" C GLU L 96 " 0.034 2.00e-02 2.50e+03 pdb=" O GLU L 96 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP L 97 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 71 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C ILE K 71 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE K 71 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS K 72 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN L 80 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C GLN L 80 " 0.028 2.00e-02 2.50e+03 pdb=" O GLN L 80 " -0.011 2.00e-02 2.50e+03 pdb=" N MET L 81 " -0.009 2.00e-02 2.50e+03 ... (remaining 600 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 782 2.78 - 3.31: 3734 3.31 - 3.84: 5690 3.84 - 4.37: 6055 4.37 - 4.90: 9558 Nonbonded interactions: 25819 Sorted by model distance: nonbonded pdb=" NE2 HIS K 158 " pdb=" O MET L 87 " model vdw 2.244 3.120 nonbonded pdb=" O ILE M 26 " pdb=" OG SER M 29 " model vdw 2.292 3.040 nonbonded pdb=" O LEU K 136 " pdb=" OG1 THR K 139 " model vdw 2.302 3.040 nonbonded pdb=" OE2 GLU K 111 " pdb=" NH2 ARG M 110 " model vdw 2.313 3.120 nonbonded pdb=" O VAL L 61 " pdb=" OG SER L 64 " model vdw 2.318 3.040 ... (remaining 25814 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: 6.290 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.950 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 : 0.006 0.039 3456 Z= 0.393 Angle : 0.793 8.648 4674 Z= 0.488 Chirality : 0.046 0.224 508 Planarity : 0.005 0.035 603 Dihedral : 15.254 83.733 1299 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % 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: -1.99 (0.36), residues: 413 helix: -0.76 (0.26), residues: 277 sheet: None (None), residues: 0 loop : -2.31 (0.50), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 176 HIS 0.011 0.003 HIS K 172 PHE 0.021 0.003 PHE M 69 TYR 0.015 0.002 TYR K 145 ARG 0.005 0.001 ARG L 54 *********************** 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 99 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.8492 (mtt180) cc_final: 0.8240 (mtm-85) REVERT: K 48 LYS cc_start: 0.8520 (mmmt) cc_final: 0.8219 (tttt) REVERT: K 106 ASN cc_start: 0.7972 (m-40) cc_final: 0.7596 (m-40) REVERT: K 134 MET cc_start: 0.8654 (ttm) cc_final: 0.8360 (ttm) REVERT: K 164 MET cc_start: 0.8939 (tpp) cc_final: 0.7063 (tpp) REVERT: L 78 LEU cc_start: 0.9094 (tp) cc_final: 0.8834 (tt) REVERT: L 94 LYS cc_start: 0.8979 (tmmt) cc_final: 0.8715 (tmmt) REVERT: M 17 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8976 (mm-30) REVERT: M 55 TYR cc_start: 0.9345 (t80) cc_final: 0.9067 (t80) REVERT: M 111 ILE cc_start: 0.9270 (mt) cc_final: 0.9066 (mt) REVERT: M 148 LYS cc_start: 0.8884 (ttpt) cc_final: 0.8656 (ttpp) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2264 time to fit residues: 25.7607 Evaluate side-chains 64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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: 7.9990 chunk 30 optimal weight: 0.0980 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN K 130 ASN K 153 ASN K 180 HIS L 80 GLN ** M 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3456 Z= 0.192 Angle : 0.643 7.231 4674 Z= 0.340 Chirality : 0.043 0.147 508 Planarity : 0.005 0.037 603 Dihedral : 4.612 21.808 452 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.38 % Allowed : 13.52 % Favored : 83.10 % 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: 0.63 (0.41), residues: 413 helix: 1.20 (0.30), residues: 289 sheet: None (None), residues: 0 loop : -1.43 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 53 HIS 0.008 0.002 HIS K 172 PHE 0.022 0.002 PHE M 15 TYR 0.024 0.001 TYR M 85 ARG 0.005 0.001 ARG L 54 *********************** 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 104 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.8264 (mtt180) cc_final: 0.7930 (mtm-85) REVERT: K 48 LYS cc_start: 0.8559 (mmmt) cc_final: 0.8254 (tttt) REVERT: K 90 LEU cc_start: 0.8142 (tp) cc_final: 0.7877 (tt) REVERT: K 126 ASP cc_start: 0.7742 (p0) cc_final: 0.7402 (p0) REVERT: K 129 ARG cc_start: 0.8730 (mtm-85) cc_final: 0.8204 (mtm-85) REVERT: K 146 ARG cc_start: 0.8489 (tmm-80) cc_final: 0.7919 (ttt-90) REVERT: K 164 MET cc_start: 0.8794 (tpp) cc_final: 0.7885 (tpp) REVERT: K 167 ARG cc_start: 0.8910 (mtm180) cc_final: 0.8685 (mtm180) REVERT: M 118 MET cc_start: 0.8378 (tpp) cc_final: 0.8117 (tpp) outliers start: 12 outliers final: 7 residues processed: 98 average time/residue: 0.1821 time to fit residues: 21.0841 Evaluate side-chains 76 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 73 PHE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 157 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.0020 chunk 24 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 102 GLN M 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3456 Z= 0.186 Angle : 0.639 8.028 4674 Z= 0.330 Chirality : 0.045 0.343 508 Planarity : 0.004 0.039 603 Dihedral : 4.357 19.027 452 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.23 % Allowed : 18.03 % Favored : 77.75 % 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: 1.42 (0.41), residues: 413 helix: 1.79 (0.30), residues: 289 sheet: None (None), residues: 0 loop : -1.10 (0.56), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 53 HIS 0.010 0.002 HIS K 158 PHE 0.012 0.001 PHE K 24 TYR 0.033 0.001 TYR M 85 ARG 0.003 0.000 ARG L 54 *********************** 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 93 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.8229 (mtt180) cc_final: 0.7941 (mtm-85) REVERT: K 48 LYS cc_start: 0.8569 (mmmt) cc_final: 0.8093 (tttt) REVERT: K 90 LEU cc_start: 0.8203 (tp) cc_final: 0.7966 (tt) REVERT: K 129 ARG cc_start: 0.8682 (mtm-85) cc_final: 0.7858 (mtm-85) REVERT: K 130 ASN cc_start: 0.8630 (m-40) cc_final: 0.8188 (m110) REVERT: K 146 ARG cc_start: 0.8553 (tmm-80) cc_final: 0.8091 (ttt-90) REVERT: K 164 MET cc_start: 0.8833 (tpp) cc_final: 0.7913 (tpp) REVERT: K 167 ARG cc_start: 0.8932 (mtm180) cc_final: 0.8610 (mtm180) REVERT: L 87 MET cc_start: 0.5885 (mmt) cc_final: 0.5554 (mmt) REVERT: M 60 VAL cc_start: 0.7888 (t) cc_final: 0.7652 (p) REVERT: M 118 MET cc_start: 0.8233 (tpp) cc_final: 0.8027 (tpp) outliers start: 15 outliers final: 10 residues processed: 85 average time/residue: 0.1847 time to fit residues: 18.5544 Evaluate side-chains 78 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 132 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 76 PHE Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 157 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.0470 chunk 17 optimal weight: 0.4980 chunk 24 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 106 ASN M 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3456 Z= 0.168 Angle : 0.598 11.604 4674 Z= 0.303 Chirality : 0.042 0.316 508 Planarity : 0.004 0.037 603 Dihedral : 4.225 18.110 452 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.82 % Allowed : 19.15 % Favored : 78.03 % 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: 1.85 (0.41), residues: 413 helix: 2.11 (0.30), residues: 285 sheet: None (None), residues: 0 loop : -0.84 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 176 HIS 0.008 0.002 HIS K 158 PHE 0.021 0.001 PHE M 15 TYR 0.025 0.001 TYR M 85 ARG 0.003 0.000 ARG K 146 *********************** 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 84 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.8215 (mtt180) cc_final: 0.7907 (mtm-85) REVERT: K 48 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8141 (tttt) REVERT: K 90 LEU cc_start: 0.8161 (tp) cc_final: 0.7933 (tt) REVERT: K 129 ARG cc_start: 0.8648 (mtm-85) cc_final: 0.8025 (mtm-85) REVERT: K 130 ASN cc_start: 0.8631 (m-40) cc_final: 0.8261 (m110) REVERT: K 146 ARG cc_start: 0.8550 (tmm-80) cc_final: 0.8012 (ttt-90) REVERT: K 164 MET cc_start: 0.8856 (tpp) cc_final: 0.7864 (tpp) REVERT: K 167 ARG cc_start: 0.8935 (mtm180) cc_final: 0.8647 (mtm180) REVERT: L 82 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.6655 (t80) REVERT: L 87 MET cc_start: 0.5781 (mmt) cc_final: 0.5419 (mmt) REVERT: M 60 VAL cc_start: 0.7966 (t) cc_final: 0.7688 (p) outliers start: 10 outliers final: 5 residues processed: 78 average time/residue: 0.1865 time to fit residues: 17.3204 Evaluate side-chains 71 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 132 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 76 PHE Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 157 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3456 Z= 0.231 Angle : 0.631 15.269 4674 Z= 0.323 Chirality : 0.041 0.148 508 Planarity : 0.004 0.039 603 Dihedral : 4.279 18.754 452 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.10 % Allowed : 20.85 % Favored : 76.06 % 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: 1.92 (0.41), residues: 413 helix: 2.15 (0.29), residues: 286 sheet: None (None), residues: 0 loop : -0.81 (0.54), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 176 HIS 0.007 0.002 HIS K 158 PHE 0.013 0.001 PHE K 24 TYR 0.017 0.001 TYR M 85 ARG 0.006 0.001 ARG K 166 *********************** 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 75 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.8177 (mtt180) cc_final: 0.7842 (mtm-85) REVERT: K 48 LYS cc_start: 0.8536 (mmmt) cc_final: 0.8151 (tttt) REVERT: K 129 ARG cc_start: 0.8683 (mtm-85) cc_final: 0.8144 (mtm-85) REVERT: K 130 ASN cc_start: 0.8660 (m-40) cc_final: 0.8313 (m110) REVERT: K 146 ARG cc_start: 0.8598 (tmm-80) cc_final: 0.8037 (ttt-90) REVERT: K 164 MET cc_start: 0.8921 (tpp) cc_final: 0.7801 (tpp) REVERT: K 167 ARG cc_start: 0.8971 (mtm180) cc_final: 0.8684 (mtm180) REVERT: L 82 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.6849 (t80) REVERT: L 87 MET cc_start: 0.5790 (mmt) cc_final: 0.5485 (mmt) REVERT: M 60 VAL cc_start: 0.8138 (t) cc_final: 0.7874 (p) outliers start: 11 outliers final: 10 residues processed: 72 average time/residue: 0.1737 time to fit residues: 15.0359 Evaluate side-chains 72 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 132 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 76 PHE Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 131 THR 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: 1.9990 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 37 optimal weight: 0.0670 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 28 optimal weight: 0.0030 overall best weight: 0.9932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3456 Z= 0.160 Angle : 0.565 12.697 4674 Z= 0.290 Chirality : 0.039 0.166 508 Planarity : 0.004 0.036 603 Dihedral : 4.034 17.680 452 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.82 % Allowed : 21.69 % Favored : 75.49 % 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: 2.18 (0.42), residues: 413 helix: 2.29 (0.30), residues: 292 sheet: None (None), residues: 0 loop : -0.70 (0.58), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 12 HIS 0.006 0.002 HIS K 172 PHE 0.025 0.001 PHE M 15 TYR 0.018 0.001 TYR M 85 ARG 0.004 0.000 ARG K 166 *********************** 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 87 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7863 (mtm-85) REVERT: K 48 LYS cc_start: 0.8471 (mmmt) cc_final: 0.8124 (tttt) REVERT: K 130 ASN cc_start: 0.8660 (m-40) cc_final: 0.8375 (m110) REVERT: K 146 ARG cc_start: 0.8634 (tmm-80) cc_final: 0.8430 (tmm-80) REVERT: K 167 ARG cc_start: 0.8964 (mtm180) cc_final: 0.8749 (mtm180) REVERT: L 82 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.6972 (t80) REVERT: L 87 MET cc_start: 0.5663 (mmt) cc_final: 0.5399 (mmt) REVERT: M 130 MET cc_start: 0.7640 (tmm) cc_final: 0.7341 (tmm) outliers start: 10 outliers final: 6 residues processed: 84 average time/residue: 0.1864 time to fit residues: 18.5600 Evaluate side-chains 70 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 132 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 131 THR 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: 4.9990 chunk 32 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 19 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7962 moved from start: 0.3819 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= 0.170 Angle : 0.636 14.359 4674 Z= 0.317 Chirality : 0.039 0.125 508 Planarity : 0.004 0.036 603 Dihedral : 3.962 17.018 452 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.97 % Allowed : 25.35 % Favored : 72.68 % 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: 2.37 (0.42), residues: 413 helix: 2.46 (0.30), residues: 286 sheet: None (None), residues: 0 loop : -0.55 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 176 HIS 0.005 0.001 HIS K 158 PHE 0.008 0.001 PHE K 24 TYR 0.019 0.001 TYR M 85 ARG 0.004 0.000 ARG K 166 *********************** 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 77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.8188 (mtt180) cc_final: 0.7876 (mtm-85) REVERT: K 48 LYS cc_start: 0.8481 (mmmt) cc_final: 0.8132 (tttt) REVERT: K 129 ARG cc_start: 0.8425 (ptp-110) cc_final: 0.8176 (ptp-110) REVERT: K 130 ASN cc_start: 0.8700 (m-40) cc_final: 0.8259 (m-40) REVERT: L 82 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.7307 (t80) REVERT: L 87 MET cc_start: 0.5648 (mmt) cc_final: 0.5394 (mmt) REVERT: M 130 MET cc_start: 0.7672 (tmm) cc_final: 0.7325 (tmm) outliers start: 7 outliers final: 6 residues processed: 74 average time/residue: 0.1934 time to fit residues: 16.9614 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 : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 132 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 76 PHE Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 131 THR 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: 3.9990 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.0050 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 106 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3456 Z= 0.163 Angle : 0.621 14.832 4674 Z= 0.308 Chirality : 0.039 0.127 508 Planarity : 0.004 0.036 603 Dihedral : 3.868 17.259 452 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.25 % Allowed : 25.92 % Favored : 71.83 % 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: 2.27 (0.41), residues: 413 helix: 2.37 (0.29), residues: 286 sheet: None (None), residues: 0 loop : -0.55 (0.55), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 12 HIS 0.004 0.001 HIS K 172 PHE 0.025 0.001 PHE M 15 TYR 0.019 0.001 TYR M 85 ARG 0.004 0.000 ARG K 146 *********************** 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 80 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.8199 (mtt180) cc_final: 0.7874 (mtm-85) REVERT: K 48 LYS cc_start: 0.8476 (mmmt) cc_final: 0.8122 (tttt) REVERT: K 129 ARG cc_start: 0.8431 (ptp-110) cc_final: 0.8184 (ptp-110) REVERT: K 130 ASN cc_start: 0.8681 (m-40) cc_final: 0.8227 (m-40) REVERT: L 87 MET cc_start: 0.5566 (mmt) cc_final: 0.5345 (mmt) REVERT: M 130 MET cc_start: 0.7604 (tmm) cc_final: 0.7243 (tmm) outliers start: 8 outliers final: 6 residues processed: 76 average time/residue: 0.2007 time to fit residues: 18.2063 Evaluate side-chains 75 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 132 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 76 PHE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 131 THR 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: 0.7980 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 36 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.0770 chunk 25 optimal weight: 0.0870 overall best weight: 0.8718 ------------------------------------------------------------------------------- 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: 0.7949 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3456 Z= 0.179 Angle : 0.669 14.762 4674 Z= 0.332 Chirality : 0.040 0.125 508 Planarity : 0.004 0.036 603 Dihedral : 3.845 17.211 452 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.97 % Allowed : 26.48 % Favored : 71.55 % 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: 2.29 (0.41), residues: 413 helix: 2.37 (0.29), residues: 292 sheet: None (None), residues: 0 loop : -0.67 (0.57), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 176 HIS 0.004 0.001 HIS K 172 PHE 0.007 0.001 PHE K 24 TYR 0.019 0.001 TYR M 85 ARG 0.012 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 76 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.8196 (mtt180) cc_final: 0.7870 (mtm-85) REVERT: K 48 LYS cc_start: 0.8478 (mmmt) cc_final: 0.8121 (tttt) REVERT: K 129 ARG cc_start: 0.8434 (ptp-110) cc_final: 0.8187 (ptp-110) REVERT: K 130 ASN cc_start: 0.8662 (m-40) cc_final: 0.8190 (m-40) REVERT: L 87 MET cc_start: 0.5518 (mmt) cc_final: 0.5289 (mmt) outliers start: 7 outliers final: 7 residues processed: 72 average time/residue: 0.1859 time to fit residues: 15.9664 Evaluate side-chains 74 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 132 ILE Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 76 PHE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 131 THR 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: 3.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 106 ASN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3456 Z= 0.177 Angle : 0.663 14.811 4674 Z= 0.328 Chirality : 0.039 0.122 508 Planarity : 0.004 0.036 603 Dihedral : 3.903 17.304 452 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.97 % Allowed : 26.76 % Favored : 71.27 % 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: 2.21 (0.41), residues: 413 helix: 2.27 (0.29), residues: 292 sheet: None (None), residues: 0 loop : -0.57 (0.58), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 12 HIS 0.004 0.001 HIS K 172 PHE 0.013 0.001 PHE K 77 TYR 0.022 0.001 TYR M 85 ARG 0.005 0.001 ARG K 146 ********************** 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 : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.8226 (mtt180) cc_final: 0.7896 (mtm-85) REVERT: K 48 LYS cc_start: 0.8497 (mmmt) cc_final: 0.8136 (tttt) REVERT: K 129 ARG cc_start: 0.8446 (ptp-110) cc_final: 0.8143 (ptp-110) REVERT: K 130 ASN cc_start: 0.8680 (m-40) cc_final: 0.8216 (m-40) outliers start: 7 outliers final: 6 residues processed: 70 average time/residue: 0.1903 time to fit residues: 15.9370 Evaluate side-chains 70 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 132 ILE Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 76 PHE Chi-restraints excluded: chain M residue 131 THR 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: 5.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 0.0670 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 59 ASN M 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.077571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.068451 restraints weight = 20089.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.069714 restraints weight = 10629.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.070510 restraints weight = 6523.303| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3456 Z= 0.180 Angle : 0.690 14.795 4674 Z= 0.341 Chirality : 0.039 0.131 508 Planarity : 0.004 0.036 603 Dihedral : 3.971 17.070 452 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.69 % Allowed : 27.61 % Favored : 70.70 % 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: 2.34 (0.30), residues: 286 sheet: None (None), residues: 0 loop : -0.56 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 53 HIS 0.003 0.001 HIS K 158 PHE 0.008 0.001 PHE K 24 TYR 0.019 0.001 TYR M 85 ARG 0.005 0.001 ARG K 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1751.73 seconds wall clock time: 32 minutes 26.02 seconds (1946.02 seconds total)