Starting phenix.real_space_refine on Tue Feb 13 05:51:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9r_34578/02_2024/8h9r_34578.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9r_34578/02_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_34578/02_2024/8h9r_34578.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9r_34578/02_2024/8h9r_34578.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9r_34578/02_2024/8h9r_34578.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9r_34578/02_2024/8h9r_34578.pdb" } 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 Residue "K GLU 20": "OE1" <-> "OE2" Residue "K PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 87": "OE1" <-> "OE2" Residue "K TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 142": "OE1" <-> "OE2" Residue "K TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 178": "OE1" <-> "OE2" Residue "L PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 86": "OD1" <-> "OD2" Residue "M ASP 11": "OD1" <-> "OD2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "M GLU 35": "OE1" <-> "OE2" Residue "M ASP 90": "OD1" <-> "OD2" Residue "M GLU 92": "OE1" <-> "OE2" Residue "M ASP 96": "OD1" <-> "OD2" Residue "M PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 2.26, per 1000 atoms: 0.67 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 571.7 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: 0.28 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: 0.80 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 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: 99.02 - 106.02: 87 106.02 - 113.01: 1860 113.01 - 120.01: 1280 120.01 - 127.01: 1408 127.01 - 134.01: 39 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 2.520 nonbonded pdb=" O ILE M 26 " pdb=" OG SER M 29 " model vdw 2.292 2.440 nonbonded pdb=" O LEU K 136 " pdb=" OG1 THR K 139 " model vdw 2.302 2.440 nonbonded pdb=" OE2 GLU K 111 " pdb=" NH2 ARG M 110 " model vdw 2.313 2.520 nonbonded pdb=" O VAL L 61 " pdb=" OG SER L 64 " model vdw 2.318 2.440 ... (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 ========== 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: 5.400 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: 26.810 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.690 Find NCS groups from input model: 0.090 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.850 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.408 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: 0.2240 time to fit residues: 25.4335 Evaluate side-chains 64 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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: 0.4980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.8012 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3456 Z= 0.199 Angle : 0.623 6.672 4674 Z= 0.332 Chirality : 0.042 0.147 508 Planarity : 0.004 0.039 603 Dihedral : 4.750 23.402 452 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.82 % Allowed : 16.90 % Favored : 80.28 % 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: 0.58 (0.41), residues: 413 helix: 1.20 (0.30), residues: 287 sheet: None (None), residues: 0 loop : -1.50 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 53 HIS 0.008 0.002 HIS K 172 PHE 0.018 0.002 PHE M 15 TYR 0.022 0.002 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 96 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.8311 (mtt180) cc_final: 0.7968 (mtm-85) REVERT: K 48 LYS cc_start: 0.8561 (mmmt) cc_final: 0.8261 (tttt) REVERT: K 90 LEU cc_start: 0.8170 (tp) cc_final: 0.7867 (tt) REVERT: K 126 ASP cc_start: 0.7769 (p0) cc_final: 0.7392 (p0) REVERT: K 134 MET cc_start: 0.8634 (ttm) cc_final: 0.8240 (ttm) REVERT: K 146 ARG cc_start: 0.8281 (tmm-80) cc_final: 0.7696 (ttt-90) REVERT: K 164 MET cc_start: 0.8789 (tpp) cc_final: 0.7856 (tpp) REVERT: K 167 ARG cc_start: 0.8857 (mtm180) cc_final: 0.8603 (mtm180) REVERT: M 37 LEU cc_start: 0.9550 (mt) cc_final: 0.8850 (mp) REVERT: M 118 MET cc_start: 0.8391 (tpp) cc_final: 0.8121 (tpp) outliers start: 10 outliers final: 5 residues processed: 90 average time/residue: 0.1851 time to fit residues: 19.6016 Evaluate side-chains 74 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain M residue 34 ASN 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 0.1980 chunk 35 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.0030 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 102 GLN ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3456 Z= 0.177 Angle : 0.615 8.325 4674 Z= 0.321 Chirality : 0.044 0.310 508 Planarity : 0.004 0.039 603 Dihedral : 4.469 22.121 452 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.94 % Allowed : 17.75 % Favored : 78.31 % 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: 1.44 (0.42), residues: 413 helix: 1.79 (0.30), residues: 289 sheet: None (None), residues: 0 loop : -1.08 (0.57), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 12 HIS 0.007 0.002 HIS K 172 PHE 0.011 0.001 PHE K 24 TYR 0.013 0.001 TYR K 26 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 92 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.8314 (mtt180) cc_final: 0.7989 (mtm-85) REVERT: K 48 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8279 (tttt) REVERT: K 90 LEU cc_start: 0.8223 (tp) cc_final: 0.7903 (tt) REVERT: K 129 ARG cc_start: 0.8682 (mtm-85) cc_final: 0.7814 (mtm-85) REVERT: K 130 ASN cc_start: 0.8638 (m-40) cc_final: 0.8270 (m-40) REVERT: K 134 MET cc_start: 0.8629 (ttm) cc_final: 0.8384 (ttm) REVERT: K 146 ARG cc_start: 0.8316 (tmm-80) cc_final: 0.7724 (ttt-90) REVERT: K 157 TYR cc_start: 0.8873 (t80) cc_final: 0.8185 (t80) REVERT: M 60 VAL cc_start: 0.7886 (t) cc_final: 0.7675 (p) REVERT: M 118 MET cc_start: 0.8261 (tpp) cc_final: 0.8060 (tpp) REVERT: M 130 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8243 (ttt) outliers start: 14 outliers final: 9 residues processed: 86 average time/residue: 0.2033 time to fit residues: 20.5278 Evaluate side-chains 78 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 108 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 89 VAL Chi-restraints excluded: chain M residue 130 MET 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: 0.0980 chunk 17 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3051 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= 0.204 Angle : 0.622 12.257 4674 Z= 0.317 Chirality : 0.044 0.300 508 Planarity : 0.004 0.039 603 Dihedral : 4.407 21.134 452 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.23 % Allowed : 19.15 % Favored : 76.62 % 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: 1.63 (0.41), residues: 413 helix: 1.97 (0.29), residues: 286 sheet: None (None), residues: 0 loop : -1.01 (0.55), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 176 HIS 0.007 0.002 HIS K 172 PHE 0.020 0.002 PHE M 15 TYR 0.012 0.001 TYR K 145 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 84 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.8278 (mtt180) cc_final: 0.7931 (mtm-85) REVERT: K 48 LYS cc_start: 0.8569 (mmmt) cc_final: 0.8236 (tttt) REVERT: K 129 ARG cc_start: 0.8688 (mtm-85) cc_final: 0.8018 (mtm-85) REVERT: K 130 ASN cc_start: 0.8620 (m-40) cc_final: 0.8286 (m110) REVERT: K 134 MET cc_start: 0.8653 (ttm) cc_final: 0.8394 (ttm) REVERT: K 146 ARG cc_start: 0.8279 (tmm-80) cc_final: 0.7665 (ttt-90) REVERT: K 164 MET cc_start: 0.9008 (tpp) cc_final: 0.6998 (tpp) REVERT: L 82 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.6671 (t80) REVERT: M 17 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8957 (mm-30) REVERT: M 60 VAL cc_start: 0.7934 (t) cc_final: 0.7719 (p) REVERT: M 118 MET cc_start: 0.8255 (tpp) cc_final: 0.8048 (tpp) REVERT: M 130 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8228 (ttt) outliers start: 15 outliers final: 10 residues processed: 77 average time/residue: 0.1952 time to fit residues: 17.6207 Evaluate side-chains 76 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 50 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 67 ASP Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 131 THR 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: 3.9990 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.0050 chunk 26 optimal weight: 0.0370 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 overall best weight: 0.5876 ------------------------------------------------------------------------------- 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: 0.7953 moved from start: 0.3373 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= 0.154 Angle : 0.605 13.883 4674 Z= 0.299 Chirality : 0.041 0.277 508 Planarity : 0.004 0.036 603 Dihedral : 4.134 19.862 452 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.97 % Allowed : 23.10 % 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: 2.13 (0.41), residues: 413 helix: 2.30 (0.30), residues: 285 sheet: None (None), residues: 0 loop : -0.69 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 12 HIS 0.006 0.001 HIS K 172 PHE 0.007 0.001 PHE K 24 TYR 0.022 0.001 TYR K 26 ARG 0.007 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 86 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.8263 (mtt180) cc_final: 0.7917 (mtm-85) REVERT: K 48 LYS cc_start: 0.8561 (mmmt) cc_final: 0.8258 (tttt) REVERT: K 90 LEU cc_start: 0.8216 (tp) cc_final: 0.7988 (tt) REVERT: K 129 ARG cc_start: 0.8713 (mtm-85) cc_final: 0.7957 (mtm-85) REVERT: K 130 ASN cc_start: 0.8617 (m-40) cc_final: 0.8259 (m110) REVERT: K 134 MET cc_start: 0.8638 (ttm) cc_final: 0.8101 (ttm) REVERT: K 166 ARG cc_start: 0.8838 (ttp80) cc_final: 0.8598 (ttp80) REVERT: K 179 LYS cc_start: 0.8387 (ptpt) cc_final: 0.8126 (ptpp) REVERT: L 82 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.6899 (t80) REVERT: L 87 MET cc_start: 0.6399 (mmt) cc_final: 0.6071 (mmt) REVERT: M 41 LEU cc_start: 0.9072 (tt) cc_final: 0.8766 (tp) REVERT: M 118 MET cc_start: 0.8193 (tpp) cc_final: 0.7987 (tpp) outliers start: 7 outliers final: 5 residues processed: 82 average time/residue: 0.1893 time to fit residues: 18.2937 Evaluate side-chains 73 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 66 VAL Chi-restraints excluded: chain M residue 80 VAL 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: 4.9990 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3456 Z= 0.155 Angle : 0.626 13.818 4674 Z= 0.308 Chirality : 0.040 0.170 508 Planarity : 0.004 0.036 603 Dihedral : 4.049 20.296 452 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.69 % Allowed : 26.20 % Favored : 72.11 % 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: 2.25 (0.42), residues: 413 helix: 2.38 (0.30), residues: 286 sheet: None (None), residues: 0 loop : -0.60 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 103 HIS 0.004 0.001 HIS K 172 PHE 0.009 0.001 PHE K 24 TYR 0.004 0.001 TYR M 151 ARG 0.006 0.001 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 82 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.8172 (mtt180) cc_final: 0.7851 (mtm-85) REVERT: K 48 LYS cc_start: 0.8559 (mmmt) cc_final: 0.8240 (tttt) REVERT: K 90 LEU cc_start: 0.8198 (tp) cc_final: 0.7973 (tt) REVERT: K 130 ASN cc_start: 0.8607 (m-40) cc_final: 0.8288 (m110) REVERT: K 134 MET cc_start: 0.8676 (ttm) cc_final: 0.8419 (ttm) REVERT: K 146 ARG cc_start: 0.8334 (tmm-80) cc_final: 0.7264 (ttp80) REVERT: L 82 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.7116 (t80) REVERT: L 87 MET cc_start: 0.6411 (mmt) cc_final: 0.6123 (mmt) REVERT: M 37 LEU cc_start: 0.9593 (mt) cc_final: 0.9229 (mp) REVERT: M 41 LEU cc_start: 0.9088 (tt) cc_final: 0.8880 (tp) REVERT: M 118 MET cc_start: 0.8217 (tpp) cc_final: 0.8015 (tpp) REVERT: M 148 LYS cc_start: 0.8586 (mtpt) cc_final: 0.8333 (mtmm) outliers start: 6 outliers final: 4 residues processed: 81 average time/residue: 0.1833 time to fit residues: 17.6025 Evaluate side-chains 76 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain M residue 66 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: 3.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3456 Z= 0.232 Angle : 0.636 15.028 4674 Z= 0.325 Chirality : 0.042 0.182 508 Planarity : 0.004 0.037 603 Dihedral : 4.228 19.529 452 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.38 % Allowed : 25.63 % Favored : 70.99 % 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: 2.20 (0.42), residues: 413 helix: 2.30 (0.30), residues: 286 sheet: None (None), residues: 0 loop : -0.52 (0.58), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 176 HIS 0.006 0.001 HIS K 172 PHE 0.021 0.002 PHE M 15 TYR 0.013 0.001 TYR K 26 ARG 0.008 0.001 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 82 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.8201 (mtt180) cc_final: 0.7890 (mtm-85) REVERT: K 48 LYS cc_start: 0.8569 (mmmt) cc_final: 0.8239 (tttt) REVERT: K 90 LEU cc_start: 0.8317 (tp) cc_final: 0.8021 (tt) REVERT: K 129 ARG cc_start: 0.8394 (ptp-110) cc_final: 0.7936 (ptp-110) REVERT: K 130 ASN cc_start: 0.8801 (m-40) cc_final: 0.8413 (m-40) REVERT: K 134 MET cc_start: 0.8708 (ttm) cc_final: 0.8304 (ttm) REVERT: L 82 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7194 (t80) REVERT: L 87 MET cc_start: 0.6461 (mmt) cc_final: 0.6188 (mmt) REVERT: M 118 MET cc_start: 0.8295 (tpp) cc_final: 0.8093 (tpp) REVERT: M 130 MET cc_start: 0.7789 (tmm) cc_final: 0.7559 (tmm) outliers start: 12 outliers final: 8 residues processed: 76 average time/residue: 0.2141 time to fit residues: 19.7272 Evaluate side-chains 74 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 66 VAL Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 73 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: 2.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 23 optimal weight: 0.0270 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3886 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= 0.172 Angle : 0.670 14.891 4674 Z= 0.322 Chirality : 0.041 0.198 508 Planarity : 0.004 0.036 603 Dihedral : 4.081 18.459 452 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.97 % Allowed : 26.20 % 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: 2.24 (0.41), residues: 413 helix: 2.29 (0.30), residues: 287 sheet: None (None), residues: 0 loop : -0.40 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 12 HIS 0.005 0.001 HIS K 172 PHE 0.024 0.001 PHE M 15 TYR 0.007 0.001 TYR K 145 ARG 0.007 0.000 ARG K 166 *********************** 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 82 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.8183 (mtt180) cc_final: 0.7864 (mtm-85) REVERT: K 48 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8240 (tttt) REVERT: K 90 LEU cc_start: 0.8296 (tp) cc_final: 0.8019 (tt) REVERT: K 129 ARG cc_start: 0.8371 (ptp-110) cc_final: 0.7988 (ptp-110) REVERT: K 130 ASN cc_start: 0.8767 (m-40) cc_final: 0.8411 (m-40) REVERT: K 134 MET cc_start: 0.8698 (ttm) cc_final: 0.8418 (ttm) REVERT: K 146 ARG cc_start: 0.8215 (tmm160) cc_final: 0.7920 (tmt170) REVERT: K 166 ARG cc_start: 0.8813 (ttp80) cc_final: 0.8507 (ttp80) REVERT: L 82 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.7199 (t80) REVERT: L 87 MET cc_start: 0.6387 (mmt) cc_final: 0.6118 (mmt) REVERT: M 37 LEU cc_start: 0.9595 (mt) cc_final: 0.8905 (mp) REVERT: M 130 MET cc_start: 0.7679 (tmm) cc_final: 0.7366 (tmm) outliers start: 7 outliers final: 6 residues processed: 79 average time/residue: 0.1902 time to fit residues: 17.7548 Evaluate side-chains 73 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.1980 chunk 23 optimal weight: 0.4980 chunk 18 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 39 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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: 0.7932 moved from start: 0.4164 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= 0.167 Angle : 0.702 18.776 4674 Z= 0.330 Chirality : 0.040 0.194 508 Planarity : 0.004 0.035 603 Dihedral : 3.890 18.385 452 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.69 % Allowed : 26.48 % 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: 2.39 (0.42), residues: 413 helix: 2.36 (0.30), residues: 290 sheet: None (None), residues: 0 loop : -0.34 (0.58), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 12 HIS 0.004 0.001 HIS K 172 PHE 0.017 0.001 PHE K 77 TYR 0.014 0.001 TYR K 26 ARG 0.006 0.000 ARG K 166 *********************** 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 82 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.8185 (mtt180) cc_final: 0.7867 (mtm-85) REVERT: K 48 LYS cc_start: 0.8526 (mmmt) cc_final: 0.8207 (tttt) REVERT: K 90 LEU cc_start: 0.8226 (tp) cc_final: 0.7997 (tt) REVERT: K 129 ARG cc_start: 0.8422 (ptp-110) cc_final: 0.8050 (ptp-110) REVERT: K 130 ASN cc_start: 0.8719 (m-40) cc_final: 0.8361 (m-40) REVERT: K 134 MET cc_start: 0.8650 (ttm) cc_final: 0.8406 (ttm) REVERT: K 146 ARG cc_start: 0.8285 (tmm160) cc_final: 0.8071 (tmt170) REVERT: K 173 MET cc_start: 0.7712 (mmt) cc_final: 0.7447 (mmm) REVERT: L 87 MET cc_start: 0.6287 (mmt) cc_final: 0.6050 (mmt) REVERT: M 37 LEU cc_start: 0.9592 (mt) cc_final: 0.9209 (mp) REVERT: M 130 MET cc_start: 0.7629 (tmm) cc_final: 0.7351 (tmm) outliers start: 6 outliers final: 5 residues processed: 79 average time/residue: 0.1720 time to fit residues: 16.3957 Evaluate side-chains 73 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 76 PHE Chi-restraints excluded: chain M residue 66 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: 1.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.4233 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= 0.169 Angle : 0.710 17.872 4674 Z= 0.337 Chirality : 0.040 0.200 508 Planarity : 0.004 0.036 603 Dihedral : 3.898 18.121 452 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.69 % Allowed : 27.32 % Favored : 70.99 % 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: 2.38 (0.42), residues: 413 helix: 2.42 (0.30), residues: 286 sheet: None (None), residues: 0 loop : -0.41 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 176 HIS 0.003 0.001 HIS K 172 PHE 0.028 0.001 PHE M 15 TYR 0.006 0.001 TYR K 145 ARG 0.006 0.000 ARG K 166 ********************** 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 80 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 ARG cc_start: 0.8190 (mtt180) cc_final: 0.7861 (mtm-85) REVERT: K 48 LYS cc_start: 0.8498 (mmmt) cc_final: 0.8169 (tttt) REVERT: K 90 LEU cc_start: 0.8258 (tp) cc_final: 0.8011 (tt) REVERT: K 129 ARG cc_start: 0.8423 (ptp-110) cc_final: 0.8046 (ptp-110) REVERT: K 130 ASN cc_start: 0.8733 (m-40) cc_final: 0.8322 (m-40) REVERT: K 134 MET cc_start: 0.8672 (ttm) cc_final: 0.8392 (ttm) REVERT: K 146 ARG cc_start: 0.8293 (tmm160) cc_final: 0.8064 (tmt170) REVERT: L 87 MET cc_start: 0.6294 (mmt) cc_final: 0.6041 (mmt) REVERT: M 37 LEU cc_start: 0.9605 (mt) cc_final: 0.8898 (mp) REVERT: M 130 MET cc_start: 0.7655 (tmm) cc_final: 0.7365 (tmm) outliers start: 6 outliers final: 5 residues processed: 77 average time/residue: 0.1572 time to fit residues: 14.6198 Evaluate side-chains 74 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 76 PHE Chi-restraints excluded: chain M residue 66 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 22 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 0.0980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.077352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.068201 restraints weight = 20182.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.069404 restraints weight = 10553.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.070148 restraints weight = 6500.639| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3456 Z= 0.181 Angle : 0.728 17.373 4674 Z= 0.351 Chirality : 0.040 0.194 508 Planarity : 0.004 0.036 603 Dihedral : 3.897 18.245 452 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.69 % Allowed : 28.73 % Favored : 69.58 % 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: 2.48 (0.42), residues: 413 helix: 2.47 (0.30), residues: 285 sheet: None (None), residues: 0 loop : -0.29 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 176 HIS 0.003 0.001 HIS K 172 PHE 0.029 0.002 PHE M 15 TYR 0.014 0.001 TYR K 26 ARG 0.006 0.000 ARG K 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1716.12 seconds wall clock time: 31 minutes 26.41 seconds (1886.41 seconds total)