Starting phenix.real_space_refine on Thu Nov 14 02:17:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9k_34570/11_2024/8h9k_34570.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9k_34570/11_2024/8h9k_34570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9k_34570/11_2024/8h9k_34570.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9k_34570/11_2024/8h9k_34570.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9k_34570/11_2024/8h9k_34570.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9k_34570/11_2024/8h9k_34570.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 11 5.16 5 C 2176 2.51 5 N 560 2.21 5 O 634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s 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: 4.79, per 1000 atoms: 1.42 Number of scatterers: 3381 At special positions: 0 Unit cell: (56.21, 102.93, 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: 0.75 Conformation dependent library (CDL) restraints added in 411.2 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: 14 helices and 1 sheets defined 71.5% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'K' and resid 19 through 30 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 32 through 48 Processing helix chain 'K' and resid 54 through 120 removed outlier: 3.836A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix Processing helix chain 'K' and resid 122 through 182 Processing helix chain 'K' and resid 194 through 206 Processing helix chain 'L' and resid 41 through 55 removed outlier: 3.884A pdb=" N ARG L 48 " --> pdb=" O VAL L 44 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU L 49 " --> pdb=" O ASP L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 83 removed outlier: 4.146A pdb=" N ARG L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 18 removed outlier: 3.706A pdb=" N ILE M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 44 removed outlier: 3.800A pdb=" N LEU M 44 " --> pdb=" O ARG M 40 " (cutoff:3.500A) 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: 3.786A pdb=" N VAL M 89 " --> pdb=" O TYR M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 140 through 143 Processing sheet with id=AA1, first strand: chain 'K' and resid 12 through 13 235 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: 0.76 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1090 1.34 - 1.46: 550 1.46 - 1.57: 1795 1.57 - 1.69: 0 1.69 - 1.81: 21 Bond restraints: 3456 Sorted by residual: bond pdb=" N GLU K 178 " pdb=" CA GLU K 178 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.20e-02 6.94e+03 6.84e+00 bond pdb=" C PHE M 139 " pdb=" N PRO M 140 " ideal model delta sigma weight residual 1.336 1.310 0.026 1.08e-02 8.57e+03 5.77e+00 bond pdb=" N LEU K 16 " pdb=" CA LEU K 16 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.27e-02 6.20e+03 4.84e+00 bond pdb=" CB PRO M 153 " pdb=" CG PRO M 153 " ideal model delta sigma weight residual 1.506 1.451 0.055 3.90e-02 6.57e+02 2.02e+00 bond pdb=" CB GLN M 155 " pdb=" CG GLN M 155 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.50e+00 ... (remaining 3451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 4044 1.20 - 2.40: 487 2.40 - 3.60: 107 3.60 - 4.80: 27 4.80 - 6.00: 9 Bond angle restraints: 4674 Sorted by residual: angle pdb=" N ALA L 85 " pdb=" CA ALA L 85 " pdb=" C ALA L 85 " ideal model delta sigma weight residual 108.45 113.46 -5.01 1.26e+00 6.30e-01 1.58e+01 angle pdb=" C PHE M 127 " pdb=" N ASP M 128 " pdb=" CA ASP M 128 " ideal model delta sigma weight residual 122.38 116.38 6.00 1.81e+00 3.05e-01 1.10e+01 angle pdb=" N SER L 65 " pdb=" CA SER L 65 " pdb=" C SER L 65 " ideal model delta sigma weight residual 113.38 109.56 3.82 1.17e+00 7.31e-01 1.07e+01 angle pdb=" N GLU K 178 " pdb=" CA GLU K 178 " pdb=" C GLU K 178 " ideal model delta sigma weight residual 111.14 107.77 3.37 1.08e+00 8.57e-01 9.76e+00 angle pdb=" N ASP M 11 " pdb=" CA ASP M 11 " pdb=" C ASP M 11 " ideal model delta sigma weight residual 110.48 106.10 4.38 1.48e+00 4.57e-01 8.75e+00 ... (remaining 4669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 1861 16.81 - 33.61: 194 33.61 - 50.42: 41 50.42 - 67.23: 11 67.23 - 84.03: 6 Dihedral angle restraints: 2113 sinusoidal: 862 harmonic: 1251 Sorted by residual: dihedral pdb=" CA PHE L 100 " pdb=" C PHE L 100 " pdb=" N GLU L 101 " pdb=" CA GLU L 101 " ideal model delta harmonic sigma weight residual -180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+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 -160.70 -19.30 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ILE M 10 " pdb=" C ILE M 10 " pdb=" N ASP M 11 " pdb=" CA ASP M 11 " ideal model delta harmonic sigma weight residual 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 318 0.043 - 0.086: 144 0.086 - 0.128: 39 0.128 - 0.171: 4 0.171 - 0.214: 3 Chirality restraints: 508 Sorted by residual: chirality pdb=" CB VAL L 61 " pdb=" CA VAL L 61 " pdb=" CG1 VAL L 61 " pdb=" CG2 VAL L 61 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB VAL K 177 " pdb=" CA VAL K 177 " pdb=" CG1 VAL K 177 " pdb=" CG2 VAL K 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA ASP K 156 " pdb=" N ASP K 156 " pdb=" C ASP K 156 " pdb=" CB ASP K 156 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.04e-01 ... (remaining 505 not shown) Planarity restraints: 603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 82 " -0.009 2.00e-02 2.50e+03 1.30e-02 2.98e+00 pdb=" CG PHE L 82 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE L 82 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE L 82 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE L 82 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE L 82 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE L 82 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU M 44 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO M 45 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO M 45 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO M 45 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 159 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C ILE K 159 " -0.028 2.00e-02 2.50e+03 pdb=" O ILE K 159 " 0.010 2.00e-02 2.50e+03 pdb=" N SER K 160 " 0.009 2.00e-02 2.50e+03 ... (remaining 600 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 232 2.72 - 3.26: 3567 3.26 - 3.81: 5391 3.81 - 4.35: 6115 4.35 - 4.90: 10122 Nonbonded interactions: 25427 Sorted by model distance: nonbonded pdb=" NH1 ARG K 154 " pdb=" O THR L 89 " model vdw 2.169 3.120 nonbonded pdb=" OG1 THR L 56 " pdb=" O GLY L 59 " model vdw 2.217 3.040 nonbonded pdb=" NE2 GLN K 162 " pdb=" O ASN M 59 " model vdw 2.217 3.120 nonbonded pdb=" NH1 ARG K 121 " pdb=" O ILE M 18 " model vdw 2.282 3.120 nonbonded pdb=" O GLU M 102 " pdb=" OG SER M 105 " model vdw 2.313 3.040 ... (remaining 25422 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: 6.730 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.890 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 0.055 3456 Z= 0.379 Angle : 0.906 5.996 4674 Z= 0.564 Chirality : 0.051 0.214 508 Planarity : 0.005 0.041 603 Dihedral : 15.467 84.035 1299 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.35), residues: 413 helix: -1.04 (0.25), residues: 286 sheet: None (None), residues: 0 loop : -2.52 (0.52), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 53 HIS 0.005 0.001 HIS K 172 PHE 0.030 0.003 PHE L 82 TYR 0.016 0.002 TYR K 145 ARG 0.004 0.001 ARG M 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7749 (tttt) REVERT: K 77 PHE cc_start: 0.8620 (t80) cc_final: 0.8265 (t80) REVERT: K 118 VAL cc_start: 0.8101 (p) cc_final: 0.7842 (p) REVERT: K 143 ARG cc_start: 0.7379 (mtt180) cc_final: 0.6898 (mtm-85) REVERT: K 146 ARG cc_start: 0.7860 (ttm170) cc_final: 0.7505 (ttt180) REVERT: K 169 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7861 (tt0) REVERT: L 50 TYR cc_start: 0.3521 (t80) cc_final: 0.3049 (t80) REVERT: M 111 ILE cc_start: 0.8375 (mt) cc_final: 0.8143 (mt) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2248 time to fit residues: 31.3327 Evaluate side-chains 78 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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: 10.0000 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 88 GLN K 98 GLN K 103 HIS K 115 GLN L 68 GLN M 136 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2855 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= 0.199 Angle : 0.614 5.201 4674 Z= 0.337 Chirality : 0.043 0.177 508 Planarity : 0.005 0.042 603 Dihedral : 5.303 55.833 452 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.94 % Allowed : 13.52 % Favored : 82.54 % 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: 0.48 (0.41), residues: 413 helix: 1.29 (0.29), residues: 291 sheet: None (None), residues: 0 loop : -2.12 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 53 HIS 0.004 0.001 HIS K 103 PHE 0.012 0.001 PHE L 93 TYR 0.016 0.001 TYR K 148 ARG 0.003 0.001 ARG K 154 *********************** 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: 14 poor density : 90 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7908 (mmmt) cc_final: 0.7537 (tptt) REVERT: K 118 VAL cc_start: 0.8302 (p) cc_final: 0.8018 (p) REVERT: K 143 ARG cc_start: 0.7188 (mtt180) cc_final: 0.6857 (mtm-85) REVERT: K 145 TYR cc_start: 0.7360 (t80) cc_final: 0.7057 (t80) REVERT: K 146 ARG cc_start: 0.7926 (ttm170) cc_final: 0.7429 (ttt180) REVERT: K 163 ASN cc_start: 0.8576 (t0) cc_final: 0.7950 (m-40) REVERT: K 169 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7739 (tt0) REVERT: L 68 GLN cc_start: 0.7677 (tp-100) cc_final: 0.7302 (tp-100) REVERT: L 87 MET cc_start: 0.7858 (mpp) cc_final: 0.7344 (mpp) REVERT: M 118 MET cc_start: 0.7873 (tmm) cc_final: 0.7617 (tpp) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 0.2117 time to fit residues: 24.0629 Evaluate side-chains 86 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 29 optimal weight: 0.0270 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 overall best weight: 1.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN M 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3456 Z= 0.239 Angle : 0.598 5.398 4674 Z= 0.325 Chirality : 0.044 0.160 508 Planarity : 0.004 0.046 603 Dihedral : 5.235 58.024 452 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.51 % Allowed : 15.21 % 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: 1.27 (0.41), residues: 413 helix: 1.87 (0.29), residues: 289 sheet: None (None), residues: 0 loop : -1.72 (0.56), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 53 HIS 0.006 0.001 HIS K 180 PHE 0.010 0.002 PHE L 100 TYR 0.012 0.001 TYR M 85 ARG 0.002 0.000 ARG K 167 *********************** 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 100 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7959 (mmmt) cc_final: 0.7600 (tptm) REVERT: K 118 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.7990 (p) REVERT: K 145 TYR cc_start: 0.7559 (t80) cc_final: 0.7205 (t80) REVERT: K 146 ARG cc_start: 0.7967 (ttm170) cc_final: 0.7496 (ttt180) REVERT: K 150 GLU cc_start: 0.8383 (tt0) cc_final: 0.8120 (tt0) REVERT: L 68 GLN cc_start: 0.7696 (tp-100) cc_final: 0.7477 (mm-40) REVERT: L 77 LYS cc_start: 0.8839 (mmmm) cc_final: 0.8596 (mttt) REVERT: L 87 MET cc_start: 0.8033 (mpp) cc_final: 0.7678 (mmm) REVERT: M 111 ILE cc_start: 0.8613 (mt) cc_final: 0.8404 (mt) REVERT: M 118 MET cc_start: 0.7928 (tmm) cc_final: 0.7587 (tpp) outliers start: 16 outliers final: 13 residues processed: 96 average time/residue: 0.2042 time to fit residues: 22.8709 Evaluate side-chains 85 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 162 GLN M 21 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3456 Z= 0.247 Angle : 0.612 10.049 4674 Z= 0.331 Chirality : 0.043 0.181 508 Planarity : 0.004 0.044 603 Dihedral : 5.242 61.218 452 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.07 % Allowed : 16.62 % 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: 1.59 (0.41), residues: 413 helix: 2.06 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -1.43 (0.58), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 53 HIS 0.004 0.001 HIS K 172 PHE 0.008 0.001 PHE K 58 TYR 0.009 0.001 TYR L 50 ARG 0.003 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 95 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7986 (mmmt) cc_final: 0.7607 (tptm) REVERT: K 85 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8037 (tt) REVERT: K 114 GLN cc_start: 0.8142 (mm110) cc_final: 0.7863 (mm-40) REVERT: K 118 VAL cc_start: 0.8207 (OUTLIER) cc_final: 0.7805 (p) REVERT: K 145 TYR cc_start: 0.7643 (t80) cc_final: 0.7309 (t80) REVERT: K 146 ARG cc_start: 0.8001 (ttm170) cc_final: 0.7529 (ttt180) REVERT: K 150 GLU cc_start: 0.8372 (tt0) cc_final: 0.8073 (tt0) REVERT: L 68 GLN cc_start: 0.7846 (tp-100) cc_final: 0.7539 (mm-40) REVERT: L 87 MET cc_start: 0.8000 (mpp) cc_final: 0.7683 (mmm) REVERT: M 111 ILE cc_start: 0.8591 (mt) cc_final: 0.8329 (mt) REVERT: M 118 MET cc_start: 0.8087 (tmm) cc_final: 0.7712 (tpp) outliers start: 18 outliers final: 11 residues processed: 90 average time/residue: 0.1980 time to fit residues: 20.9269 Evaluate side-chains 81 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 21 GLN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3456 Z= 0.161 Angle : 0.572 8.043 4674 Z= 0.307 Chirality : 0.041 0.173 508 Planarity : 0.004 0.042 603 Dihedral : 5.061 59.334 452 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.07 % Allowed : 17.18 % 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: 2.14 (0.42), residues: 413 helix: 2.43 (0.29), residues: 289 sheet: None (None), residues: 0 loop : -1.11 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 53 HIS 0.002 0.001 HIS K 172 PHE 0.009 0.001 PHE L 100 TYR 0.010 0.001 TYR K 148 ARG 0.007 0.001 ARG K 167 *********************** 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 91 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7865 (mmmt) cc_final: 0.7515 (tptm) REVERT: K 114 GLN cc_start: 0.8121 (mm110) cc_final: 0.7844 (mm-40) REVERT: K 118 VAL cc_start: 0.8169 (OUTLIER) cc_final: 0.7652 (p) REVERT: K 145 TYR cc_start: 0.7642 (t80) cc_final: 0.7326 (t80) REVERT: K 146 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7509 (ttt180) REVERT: K 150 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8067 (tt0) REVERT: K 163 ASN cc_start: 0.8578 (t0) cc_final: 0.7973 (m-40) REVERT: L 60 PRO cc_start: 0.6831 (Cg_endo) cc_final: 0.6590 (Cg_exo) REVERT: L 87 MET cc_start: 0.7818 (mpp) cc_final: 0.7537 (mmm) REVERT: M 111 ILE cc_start: 0.8558 (mt) cc_final: 0.8277 (mt) REVERT: M 118 MET cc_start: 0.8083 (tmm) cc_final: 0.7689 (tpp) outliers start: 18 outliers final: 13 residues processed: 84 average time/residue: 0.2188 time to fit residues: 21.3751 Evaluate side-chains 83 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.0470 chunk 32 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8262 ------------------------------------------------------------------------------- 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: 0.7609 moved from start: 0.4359 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= 0.169 Angle : 0.584 10.537 4674 Z= 0.312 Chirality : 0.041 0.166 508 Planarity : 0.004 0.042 603 Dihedral : 4.940 58.119 452 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.51 % Allowed : 17.46 % 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: 2.39 (0.42), residues: 413 helix: 2.59 (0.29), residues: 289 sheet: None (None), residues: 0 loop : -0.95 (0.61), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 33 HIS 0.003 0.001 HIS K 172 PHE 0.010 0.001 PHE L 100 TYR 0.012 0.001 TYR M 85 ARG 0.002 0.000 ARG K 143 *********************** 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 93 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7858 (mmmt) cc_final: 0.7532 (tptm) REVERT: K 134 MET cc_start: 0.8409 (ttm) cc_final: 0.7937 (ttm) REVERT: K 145 TYR cc_start: 0.7705 (t80) cc_final: 0.7395 (t80) REVERT: K 146 ARG cc_start: 0.7949 (ttm170) cc_final: 0.7517 (ttt180) REVERT: K 150 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8091 (tt0) REVERT: K 163 ASN cc_start: 0.8583 (OUTLIER) cc_final: 0.7973 (m-40) REVERT: L 60 PRO cc_start: 0.6767 (Cg_endo) cc_final: 0.6526 (Cg_exo) REVERT: L 87 MET cc_start: 0.7798 (mpp) cc_final: 0.7441 (mmm) REVERT: M 111 ILE cc_start: 0.8553 (mt) cc_final: 0.8284 (mt) REVERT: M 118 MET cc_start: 0.8119 (tmm) cc_final: 0.7720 (tpp) outliers start: 16 outliers final: 13 residues processed: 88 average time/residue: 0.2058 time to fit residues: 21.3068 Evaluate side-chains 83 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.0670 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 19 optimal weight: 10.0000 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4613 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= 0.167 Angle : 0.578 10.281 4674 Z= 0.310 Chirality : 0.040 0.177 508 Planarity : 0.004 0.041 603 Dihedral : 4.840 56.165 452 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.51 % Allowed : 18.59 % Favored : 76.90 % 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: 2.59 (0.42), residues: 413 helix: 2.72 (0.29), residues: 290 sheet: None (None), residues: 0 loop : -0.87 (0.62), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 33 HIS 0.002 0.000 HIS K 180 PHE 0.012 0.001 PHE L 82 TYR 0.012 0.001 TYR M 85 ARG 0.003 0.000 ARG K 167 *********************** 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 87 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7839 (mmmt) cc_final: 0.7510 (tptm) REVERT: K 118 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7767 (p) REVERT: K 134 MET cc_start: 0.8368 (ttm) cc_final: 0.7917 (ttm) REVERT: K 145 TYR cc_start: 0.7702 (t80) cc_final: 0.7402 (t80) REVERT: K 146 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7570 (ttt180) REVERT: K 163 ASN cc_start: 0.8555 (t0) cc_final: 0.7940 (m-40) REVERT: L 60 PRO cc_start: 0.6802 (Cg_endo) cc_final: 0.6554 (Cg_exo) REVERT: L 87 MET cc_start: 0.7777 (mpp) cc_final: 0.7429 (mmm) REVERT: M 111 ILE cc_start: 0.8536 (mt) cc_final: 0.8263 (mt) REVERT: M 118 MET cc_start: 0.8126 (tmm) cc_final: 0.7729 (tpp) outliers start: 16 outliers final: 10 residues processed: 83 average time/residue: 0.2099 time to fit residues: 20.2192 Evaluate side-chains 81 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3456 Z= 0.171 Angle : 0.636 11.216 4674 Z= 0.325 Chirality : 0.041 0.173 508 Planarity : 0.004 0.041 603 Dihedral : 4.867 54.973 452 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.66 % Allowed : 20.28 % 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: 2.71 (0.42), residues: 413 helix: 2.77 (0.29), residues: 290 sheet: None (None), residues: 0 loop : -0.70 (0.63), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 33 HIS 0.002 0.001 HIS K 172 PHE 0.029 0.002 PHE L 82 TYR 0.011 0.001 TYR M 85 ARG 0.005 0.001 ARG K 167 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7864 (mmmt) cc_final: 0.7522 (tptm) REVERT: K 134 MET cc_start: 0.8374 (ttm) cc_final: 0.7927 (ttm) REVERT: K 145 TYR cc_start: 0.7698 (t80) cc_final: 0.7422 (t80) REVERT: K 146 ARG cc_start: 0.7949 (ttm170) cc_final: 0.7574 (ttt180) REVERT: K 163 ASN cc_start: 0.8490 (t0) cc_final: 0.7929 (t0) REVERT: L 55 GLN cc_start: 0.6776 (pp30) cc_final: 0.6448 (pm20) REVERT: L 60 PRO cc_start: 0.6766 (Cg_endo) cc_final: 0.6525 (Cg_exo) REVERT: L 87 MET cc_start: 0.7736 (mpp) cc_final: 0.7386 (mmm) REVERT: M 111 ILE cc_start: 0.8513 (mt) cc_final: 0.8243 (mt) REVERT: M 118 MET cc_start: 0.8127 (tmm) cc_final: 0.7738 (tpp) outliers start: 13 outliers final: 10 residues processed: 82 average time/residue: 0.1990 time to fit residues: 19.1376 Evaluate side-chains 75 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.0970 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 180 HIS ** M 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 23 GLN M 129 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 3456 Z= 0.229 Angle : 0.671 11.049 4674 Z= 0.350 Chirality : 0.041 0.167 508 Planarity : 0.004 0.041 603 Dihedral : 4.917 54.232 452 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.10 % Allowed : 21.13 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.42), residues: 413 helix: 2.84 (0.29), residues: 286 sheet: None (None), residues: 0 loop : -0.69 (0.61), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 12 HIS 0.001 0.000 HIS K 172 PHE 0.043 0.002 PHE L 82 TYR 0.012 0.001 TYR M 85 ARG 0.003 0.000 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 84 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7820 (mmmt) cc_final: 0.7489 (tptm) REVERT: K 145 TYR cc_start: 0.7711 (t80) cc_final: 0.7456 (t80) REVERT: K 146 ARG cc_start: 0.7961 (ttm170) cc_final: 0.7638 (ttt180) REVERT: K 163 ASN cc_start: 0.8518 (t0) cc_final: 0.7898 (t0) REVERT: L 48 ARG cc_start: 0.8883 (ptm160) cc_final: 0.8482 (ptt90) REVERT: L 60 PRO cc_start: 0.6724 (Cg_endo) cc_final: 0.6497 (Cg_exo) REVERT: L 87 MET cc_start: 0.7707 (mpp) cc_final: 0.7505 (mmm) REVERT: M 111 ILE cc_start: 0.8495 (mt) cc_final: 0.8219 (mt) REVERT: M 118 MET cc_start: 0.8172 (tmm) cc_final: 0.7778 (tpp) outliers start: 11 outliers final: 9 residues processed: 82 average time/residue: 0.2073 time to fit residues: 19.9604 Evaluate side-chains 77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 0.0060 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 27 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 3456 Z= 0.226 Angle : 0.697 11.713 4674 Z= 0.361 Chirality : 0.041 0.157 508 Planarity : 0.004 0.040 603 Dihedral : 4.815 52.003 452 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.54 % Allowed : 21.97 % 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: 2.85 (0.42), residues: 413 helix: 2.99 (0.29), residues: 281 sheet: None (None), residues: 0 loop : -0.66 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 33 HIS 0.004 0.001 HIS K 158 PHE 0.046 0.002 PHE L 82 TYR 0.012 0.001 TYR M 85 ARG 0.004 0.001 ARG K 167 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7812 (mmmt) cc_final: 0.7481 (tptm) REVERT: K 134 MET cc_start: 0.8307 (ttm) cc_final: 0.8051 (ttm) REVERT: K 145 TYR cc_start: 0.7707 (t80) cc_final: 0.7463 (t80) REVERT: K 146 ARG cc_start: 0.7969 (ttm170) cc_final: 0.7666 (ttt180) REVERT: K 163 ASN cc_start: 0.8510 (t0) cc_final: 0.7890 (t0) REVERT: L 49 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6935 (mt-10) REVERT: L 55 GLN cc_start: 0.6819 (pp30) cc_final: 0.6082 (pm20) REVERT: L 60 PRO cc_start: 0.6654 (Cg_endo) cc_final: 0.6437 (Cg_exo) REVERT: L 87 MET cc_start: 0.7432 (mpp) cc_final: 0.6974 (mmm) REVERT: M 111 ILE cc_start: 0.8487 (mt) cc_final: 0.8202 (mt) REVERT: M 118 MET cc_start: 0.8166 (tmm) cc_final: 0.7774 (tpp) outliers start: 9 outliers final: 7 residues processed: 80 average time/residue: 0.2186 time to fit residues: 20.4702 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 : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 0.0030 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.130911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.111755 restraints weight = 8972.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.113363 restraints weight = 5106.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.114353 restraints weight = 2539.967| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 3456 Z= 0.225 Angle : 0.711 10.932 4674 Z= 0.371 Chirality : 0.041 0.173 508 Planarity : 0.004 0.041 603 Dihedral : 4.805 51.455 452 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.54 % Allowed : 22.25 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.42), residues: 413 helix: 2.97 (0.29), residues: 281 sheet: None (None), residues: 0 loop : -0.67 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 33 HIS 0.002 0.001 HIS K 172 PHE 0.011 0.001 PHE L 82 TYR 0.010 0.001 TYR M 85 ARG 0.003 0.000 ARG K 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1731.14 seconds wall clock time: 32 minutes 5.72 seconds (1925.72 seconds total)