Starting phenix.real_space_refine on Sun Mar 10 17:04:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9n_34574/03_2024/8h9n_34574.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9n_34574/03_2024/8h9n_34574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9n_34574/03_2024/8h9n_34574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9n_34574/03_2024/8h9n_34574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9n_34574/03_2024/8h9n_34574.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9n_34574/03_2024/8h9n_34574.pdb" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 11 5.16 5 C 2176 2.51 5 N 560 2.21 5 O 634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 7": "OE1" <-> "OE2" Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 20": "OE1" <-> "OE2" Residue "K PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 83": "OD1" <-> "OD2" Residue "K GLU 95": "OE1" <-> "OE2" Residue "K TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 150": "OE1" <-> "OE2" Residue "K ASP 156": "OD1" <-> "OD2" Residue "K TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 62": "OD1" <-> "OD2" Residue "L GLU 72": "OE1" <-> "OE2" Residue "L ASP 97": "OD1" <-> "OD2" Residue "M ASP 11": "OD1" <-> "OD2" Residue "M PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M ASP 52": "OD1" <-> "OD2" Residue "M PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 90": "OD1" <-> "OD2" Residue "M GLU 92": "OE1" <-> "OE2" Residue "M ASP 96": "OD1" <-> "OD2" Residue "M GLU 115": "OE1" <-> "OE2" Residue "M PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 137": "OE1" <-> "OE2" Residue "M PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 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: 2.40, per 1000 atoms: 0.71 Number of scatterers: 3381 At special positions: 0 Unit cell: (81.03, 96.36, 207.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 11 16.00 O 634 8.00 N 560 7.00 C 2176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 1.29 Conformation dependent library (CDL) restraints added in 638.7 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: 15 helices and 1 sheets defined 72.7% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'K' and resid 19 through 30 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 32 through 48 Processing helix chain 'K' and resid 54 through 121 removed outlier: 3.900A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix Processing helix chain 'K' and resid 122 through 182 Processing helix chain 'K' and resid 194 through 206 removed outlier: 3.789A pdb=" N LEU K 201 " --> pdb=" O CYS K 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 55 Processing helix chain 'L' and resid 67 through 83 removed outlier: 4.318A pdb=" N ARG L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 18 removed outlier: 3.690A pdb=" N ILE M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 43 Processing helix chain 'M' and resid 53 through 58 Processing helix chain 'M' and resid 64 through 75 Processing helix chain 'M' and resid 85 through 123 removed outlier: 3.896A pdb=" N VAL M 89 " --> pdb=" O TYR M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 130 removed outlier: 3.690A pdb=" N MET M 130 " --> pdb=" O PHE M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 140 through 143 removed outlier: 3.662A pdb=" N LYS M 143 " --> pdb=" O PRO M 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 140 through 143' Processing sheet with id=AA1, first strand: chain 'K' and resid 12 through 13 237 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1078 1.34 - 1.45: 470 1.45 - 1.57: 1887 1.57 - 1.69: 0 1.69 - 1.80: 21 Bond restraints: 3456 Sorted by residual: bond pdb=" N LEU M 76 " pdb=" CA LEU M 76 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.25e-02 6.40e+03 6.36e+00 bond pdb=" N GLU K 178 " pdb=" CA GLU K 178 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.19e+00 bond pdb=" N LYS K 168 " pdb=" CA LYS K 168 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.89e+00 bond pdb=" CB PRO M 153 " pdb=" CG PRO M 153 " ideal model delta sigma weight residual 1.506 1.441 0.065 3.90e-02 6.57e+02 2.79e+00 bond pdb=" CB THR K 139 " pdb=" CG2 THR K 139 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.88e+00 ... (remaining 3451 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.13: 88 106.13 - 113.13: 1864 113.13 - 120.12: 1388 120.12 - 127.11: 1297 127.11 - 134.11: 37 Bond angle restraints: 4674 Sorted by residual: angle pdb=" C PHE K 125 " pdb=" N ASP K 126 " pdb=" CA ASP K 126 " ideal model delta sigma weight residual 120.31 114.62 5.69 1.52e+00 4.33e-01 1.40e+01 angle pdb=" C LYS K 72 " pdb=" N LYS K 73 " pdb=" CA LYS K 73 " ideal model delta sigma weight residual 121.80 114.95 6.85 2.16e+00 2.14e-01 1.01e+01 angle pdb=" N ARG K 121 " pdb=" CA ARG K 121 " pdb=" C ARG K 121 " ideal model delta sigma weight residual 111.75 115.44 -3.69 1.28e+00 6.10e-01 8.31e+00 angle pdb=" C ILE K 174 " pdb=" N ASN K 175 " pdb=" CA ASN K 175 " ideal model delta sigma weight residual 120.68 115.80 4.88 1.70e+00 3.46e-01 8.24e+00 angle pdb=" CA LEU K 117 " pdb=" CB LEU K 117 " pdb=" CG LEU K 117 " ideal model delta sigma weight residual 116.30 125.91 -9.61 3.50e+00 8.16e-02 7.54e+00 ... (remaining 4669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 1847 16.70 - 33.39: 210 33.39 - 50.09: 40 50.09 - 66.79: 12 66.79 - 83.49: 4 Dihedral angle restraints: 2113 sinusoidal: 862 harmonic: 1251 Sorted by residual: dihedral pdb=" CA PHE L 100 " pdb=" C PHE L 100 " pdb=" N GLU L 101 " pdb=" CA GLU L 101 " ideal model delta harmonic sigma weight residual -180.00 -161.42 -18.58 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ILE M 10 " pdb=" C ILE M 10 " pdb=" N ASP M 11 " pdb=" CA ASP M 11 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ARG K 121 " pdb=" C ARG K 121 " pdb=" N HIS K 122 " pdb=" CA HIS K 122 " ideal model delta harmonic sigma weight residual -180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 220 0.029 - 0.058: 170 0.058 - 0.087: 67 0.087 - 0.116: 31 0.116 - 0.145: 20 Chirality restraints: 508 Sorted by residual: chirality pdb=" CA VAL M 80 " pdb=" N VAL M 80 " pdb=" C VAL M 80 " pdb=" CB VAL M 80 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA PHE K 58 " pdb=" N PHE K 58 " pdb=" C PHE K 58 " pdb=" CB PHE K 58 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA PRO K 76 " pdb=" N PRO K 76 " pdb=" C PRO K 76 " pdb=" CB PRO K 76 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 505 not shown) Planarity restraints: 603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE M 69 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C PHE M 69 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE M 69 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU M 70 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 159 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C ILE K 159 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE K 159 " -0.011 2.00e-02 2.50e+03 pdb=" N SER K 160 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE M 139 " 0.014 2.00e-02 2.50e+03 1.29e-02 2.90e+00 pdb=" CG PHE M 139 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE M 139 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE M 139 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE M 139 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE M 139 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE M 139 " 0.002 2.00e-02 2.50e+03 ... (remaining 600 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 295 2.72 - 3.27: 3535 3.27 - 3.81: 5368 3.81 - 4.36: 5909 4.36 - 4.90: 10125 Nonbonded interactions: 25232 Sorted by model distance: nonbonded pdb=" O VAL K 181 " pdb=" OG SER K 184 " model vdw 2.178 2.440 nonbonded pdb=" NZ LYS K 84 " pdb=" OE1 GLU K 87 " model vdw 2.254 2.520 nonbonded pdb=" NH1 ARG K 154 " pdb=" O THR L 89 " model vdw 2.272 2.520 nonbonded pdb=" OG1 THR L 56 " pdb=" O GLY L 59 " model vdw 2.274 2.440 nonbonded pdb=" OD1 ASP K 126 " pdb=" NH2 ARG K 129 " model vdw 2.278 2.520 ... (remaining 25227 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 6.670 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: 26.840 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.420 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 3456 Z= 0.443 Angle : 0.878 9.610 4674 Z= 0.496 Chirality : 0.052 0.145 508 Planarity : 0.006 0.040 603 Dihedral : 15.253 83.485 1299 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.34), residues: 413 helix: -1.09 (0.25), residues: 285 sheet: None (None), residues: 0 loop : -2.19 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP K 176 HIS 0.006 0.003 HIS K 158 PHE 0.030 0.003 PHE M 139 TYR 0.020 0.003 TYR K 140 ARG 0.004 0.001 ARG M 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 56 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7139 (tt0) REVERT: K 154 ARG cc_start: 0.7546 (mtt-85) cc_final: 0.7256 (mtp180) REVERT: K 169 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8248 (tp30) REVERT: L 47 ILE cc_start: 0.8384 (pt) cc_final: 0.7695 (pt) REVERT: L 91 PRO cc_start: 0.7630 (Cg_endo) cc_final: 0.7350 (Cg_exo) REVERT: L 103 ILE cc_start: 0.5678 (mt) cc_final: 0.5461 (mt) REVERT: L 105 LYS cc_start: 0.5593 (tmtt) cc_final: 0.5125 (tptt) REVERT: M 96 ASP cc_start: 0.8088 (t0) cc_final: 0.7866 (t70) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2221 time to fit residues: 29.5615 Evaluate side-chains 75 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 88 GLN K 98 GLN K 103 HIS K 115 GLN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 GLN M 23 GLN M 47 ASN M 59 ASN M 136 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3456 Z= 0.231 Angle : 0.623 7.760 4674 Z= 0.336 Chirality : 0.042 0.145 508 Planarity : 0.005 0.046 603 Dihedral : 5.103 44.858 452 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.23 % Allowed : 14.37 % Favored : 81.41 % 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: 0.44 (0.41), residues: 413 helix: 1.20 (0.30), residues: 286 sheet: None (None), residues: 0 loop : -1.84 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 53 HIS 0.003 0.002 HIS K 103 PHE 0.018 0.002 PHE L 93 TYR 0.023 0.002 TYR M 56 ARG 0.005 0.001 ARG M 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 103 ILE cc_start: 0.5724 (mt) cc_final: 0.5306 (mt) REVERT: M 96 ASP cc_start: 0.7982 (t0) cc_final: 0.7732 (t70) REVERT: M 119 GLU cc_start: 0.6648 (tp30) cc_final: 0.6406 (tp30) outliers start: 15 outliers final: 10 residues processed: 92 average time/residue: 0.1889 time to fit residues: 20.3581 Evaluate side-chains 80 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain M residue 93 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 8.9990 chunk 24 optimal weight: 0.0070 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 0.0770 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 overall best weight: 0.9758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 128 GLN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3062 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= 0.181 Angle : 0.565 7.067 4674 Z= 0.304 Chirality : 0.039 0.144 508 Planarity : 0.005 0.045 603 Dihedral : 4.683 36.627 452 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 5.07 % Allowed : 17.75 % Favored : 77.18 % 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: 1.45 (0.43), residues: 413 helix: 2.01 (0.31), residues: 285 sheet: None (None), residues: 0 loop : -1.54 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 53 HIS 0.002 0.001 HIS K 158 PHE 0.021 0.002 PHE K 24 TYR 0.017 0.001 TYR K 74 ARG 0.006 0.001 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 98 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 148 TYR cc_start: 0.7795 (t80) cc_final: 0.7478 (t80) REVERT: K 169 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8334 (tp30) REVERT: L 80 GLN cc_start: 0.8313 (pp30) cc_final: 0.8111 (pt0) REVERT: L 81 MET cc_start: 0.8360 (ppp) cc_final: 0.8052 (ppp) REVERT: M 92 GLU cc_start: 0.6942 (tp30) cc_final: 0.6638 (tp30) REVERT: M 96 ASP cc_start: 0.7940 (t0) cc_final: 0.7538 (t0) REVERT: M 119 GLU cc_start: 0.6731 (tp30) cc_final: 0.6491 (tp30) outliers start: 18 outliers final: 10 residues processed: 91 average time/residue: 0.1974 time to fit residues: 21.0070 Evaluate side-chains 82 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 169 GLU Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 93 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 ** M 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3456 Z= 0.319 Angle : 0.644 5.770 4674 Z= 0.348 Chirality : 0.043 0.156 508 Planarity : 0.005 0.048 603 Dihedral : 4.671 22.741 452 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.79 % Allowed : 18.31 % 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: 1.56 (0.43), residues: 413 helix: 2.00 (0.30), residues: 291 sheet: None (None), residues: 0 loop : -1.41 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP M 53 HIS 0.004 0.002 HIS K 180 PHE 0.026 0.002 PHE K 24 TYR 0.021 0.002 TYR M 85 ARG 0.007 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 91 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 42 ILE cc_start: 0.9344 (tt) cc_final: 0.9126 (tt) REVERT: K 148 TYR cc_start: 0.7839 (t80) cc_final: 0.7236 (t80) REVERT: L 55 GLN cc_start: 0.7844 (pp30) cc_final: 0.7529 (pp30) REVERT: M 92 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6847 (tp30) REVERT: M 96 ASP cc_start: 0.7976 (t0) cc_final: 0.7627 (t70) REVERT: M 119 GLU cc_start: 0.6820 (tp30) cc_final: 0.6526 (tp30) REVERT: M 157 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7230 (mp) outliers start: 17 outliers final: 13 residues processed: 82 average time/residue: 0.1806 time to fit residues: 17.5689 Evaluate side-chains 81 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 92 GLU Chi-restraints excluded: chain M residue 93 GLU 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: 0.9980 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 26 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3456 Z= 0.204 Angle : 0.577 7.243 4674 Z= 0.309 Chirality : 0.039 0.140 508 Planarity : 0.005 0.044 603 Dihedral : 4.340 21.264 452 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.23 % Allowed : 22.25 % Favored : 73.52 % 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: 1.86 (0.43), residues: 413 helix: 2.28 (0.31), residues: 286 sheet: None (None), residues: 0 loop : -1.31 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 53 HIS 0.002 0.001 HIS K 158 PHE 0.012 0.001 PHE M 139 TYR 0.026 0.002 TYR M 85 ARG 0.004 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 87 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 42 ILE cc_start: 0.9325 (tt) cc_final: 0.9117 (tt) REVERT: K 148 TYR cc_start: 0.7800 (t80) cc_final: 0.7158 (t80) REVERT: K 165 MET cc_start: 0.8288 (mtp) cc_final: 0.6942 (tmm) REVERT: K 178 GLU cc_start: 0.8074 (mm-30) cc_final: 0.6876 (tm-30) REVERT: L 55 GLN cc_start: 0.7880 (pp30) cc_final: 0.7547 (pp30) REVERT: L 81 MET cc_start: 0.8367 (ppp) cc_final: 0.8018 (ppp) REVERT: M 92 GLU cc_start: 0.7052 (tp30) cc_final: 0.6761 (tp30) REVERT: M 96 ASP cc_start: 0.7842 (t0) cc_final: 0.7479 (t70) REVERT: M 119 GLU cc_start: 0.6805 (tp30) cc_final: 0.6493 (tp30) outliers start: 15 outliers final: 13 residues processed: 81 average time/residue: 0.1878 time to fit residues: 18.1314 Evaluate side-chains 78 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 125 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 0.0670 chunk 32 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- 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: 0.7590 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3456 Z= 0.143 Angle : 0.532 6.716 4674 Z= 0.284 Chirality : 0.038 0.136 508 Planarity : 0.005 0.042 603 Dihedral : 4.040 20.713 452 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.94 % Allowed : 24.23 % 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: 2.65 (0.43), residues: 413 helix: 2.84 (0.30), residues: 283 sheet: None (None), residues: 0 loop : -0.82 (0.58), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 53 HIS 0.001 0.000 HIS K 158 PHE 0.013 0.001 PHE L 100 TYR 0.023 0.001 TYR M 85 ARG 0.004 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 86 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 42 ILE cc_start: 0.9307 (tt) cc_final: 0.9101 (tt) REVERT: K 148 TYR cc_start: 0.7727 (t80) cc_final: 0.7176 (t80) REVERT: K 178 GLU cc_start: 0.7962 (mm-30) cc_final: 0.6857 (tm-30) REVERT: L 55 GLN cc_start: 0.7801 (pp30) cc_final: 0.7505 (pp30) REVERT: L 81 MET cc_start: 0.8300 (ppp) cc_final: 0.8001 (ppp) REVERT: M 92 GLU cc_start: 0.7027 (tp30) cc_final: 0.6709 (tp30) REVERT: M 96 ASP cc_start: 0.7840 (t0) cc_final: 0.7463 (t70) REVERT: M 119 GLU cc_start: 0.6888 (tp30) cc_final: 0.6596 (tp30) REVERT: M 157 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7096 (mp) outliers start: 14 outliers final: 8 residues processed: 79 average time/residue: 0.1870 time to fit residues: 17.4427 Evaluate side-chains 74 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 157 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.0470 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.0870 overall best weight: 0.5856 ------------------------------------------------------------------------------- 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: 0.7586 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3456 Z= 0.151 Angle : 0.573 9.824 4674 Z= 0.301 Chirality : 0.041 0.261 508 Planarity : 0.005 0.041 603 Dihedral : 3.915 20.010 452 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.94 % Allowed : 23.10 % Favored : 72.96 % 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: 2.72 (0.43), residues: 413 helix: 2.89 (0.30), residues: 283 sheet: None (None), residues: 0 loop : -0.75 (0.58), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 176 HIS 0.001 0.000 HIS K 122 PHE 0.015 0.001 PHE L 100 TYR 0.021 0.001 TYR M 85 ARG 0.003 0.000 ARG M 40 *********************** 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 fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 42 ILE cc_start: 0.9310 (tt) cc_final: 0.9108 (tt) REVERT: K 148 TYR cc_start: 0.7744 (t80) cc_final: 0.7204 (t80) REVERT: K 178 GLU cc_start: 0.7926 (mm-30) cc_final: 0.6845 (tm-30) REVERT: L 55 GLN cc_start: 0.7830 (pp30) cc_final: 0.7546 (pp30) REVERT: M 82 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7469 (pp20) REVERT: M 92 GLU cc_start: 0.6970 (tp30) cc_final: 0.6634 (tp30) REVERT: M 96 ASP cc_start: 0.7741 (t0) cc_final: 0.7413 (t70) REVERT: M 119 GLU cc_start: 0.6892 (tp30) cc_final: 0.6605 (tp30) REVERT: M 157 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.6993 (mp) outliers start: 14 outliers final: 10 residues processed: 82 average time/residue: 0.1671 time to fit residues: 16.4138 Evaluate side-chains 82 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 157 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.0470 chunk 23 optimal weight: 0.0970 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 80 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: 0.4482 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= 0.153 Angle : 0.562 6.341 4674 Z= 0.302 Chirality : 0.039 0.137 508 Planarity : 0.005 0.040 603 Dihedral : 3.841 18.704 452 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.51 % Allowed : 22.54 % Favored : 72.96 % 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: 2.92 (0.43), residues: 413 helix: 3.05 (0.30), residues: 282 sheet: None (None), residues: 0 loop : -0.70 (0.58), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 53 HIS 0.001 0.000 HIS K 172 PHE 0.023 0.001 PHE K 24 TYR 0.024 0.001 TYR M 85 ARG 0.004 0.001 ARG M 40 *********************** 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 89 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 42 ILE cc_start: 0.9311 (tt) cc_final: 0.9107 (tt) REVERT: K 148 TYR cc_start: 0.7751 (t80) cc_final: 0.7232 (t80) REVERT: L 55 GLN cc_start: 0.7829 (pp30) cc_final: 0.7574 (pp30) REVERT: M 82 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7437 (pp20) REVERT: M 92 GLU cc_start: 0.7015 (tp30) cc_final: 0.6687 (tp30) REVERT: M 96 ASP cc_start: 0.7801 (t0) cc_final: 0.7586 (t70) REVERT: M 119 GLU cc_start: 0.6876 (tp30) cc_final: 0.6556 (tp30) REVERT: M 157 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.6975 (mp) outliers start: 16 outliers final: 11 residues processed: 82 average time/residue: 0.1854 time to fit residues: 18.0087 Evaluate side-chains 81 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 157 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3456 Z= 0.171 Angle : 0.587 7.660 4674 Z= 0.320 Chirality : 0.040 0.138 508 Planarity : 0.005 0.041 603 Dihedral : 3.850 17.390 452 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.23 % Allowed : 23.66 % 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: 2.81 (0.42), residues: 413 helix: 2.94 (0.30), residues: 282 sheet: None (None), residues: 0 loop : -0.66 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 53 HIS 0.001 0.000 HIS K 172 PHE 0.021 0.001 PHE K 125 TYR 0.022 0.001 TYR M 85 ARG 0.004 0.001 ARG M 40 *********************** 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 86 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 42 ILE cc_start: 0.9312 (tt) cc_final: 0.9105 (tt) REVERT: K 120 LYS cc_start: 0.8691 (tppt) cc_final: 0.7886 (ttpt) REVERT: K 148 TYR cc_start: 0.7759 (t80) cc_final: 0.7184 (t80) REVERT: L 55 GLN cc_start: 0.7833 (pp30) cc_final: 0.7618 (pp30) REVERT: M 82 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7443 (pp20) REVERT: M 92 GLU cc_start: 0.6894 (tp30) cc_final: 0.6547 (tp30) REVERT: M 119 GLU cc_start: 0.6808 (tp30) cc_final: 0.6439 (tp30) REVERT: M 157 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.6993 (mp) outliers start: 15 outliers final: 11 residues processed: 82 average time/residue: 0.1975 time to fit residues: 19.0155 Evaluate side-chains 81 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 157 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 0.0270 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- 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: 0.7594 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3456 Z= 0.184 Angle : 0.585 6.548 4674 Z= 0.321 Chirality : 0.040 0.139 508 Planarity : 0.005 0.041 603 Dihedral : 3.913 17.257 452 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.10 % Allowed : 24.51 % Favored : 72.39 % 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: 2.54 (0.42), residues: 413 helix: 2.73 (0.30), residues: 280 sheet: None (None), residues: 0 loop : -0.69 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 12 HIS 0.002 0.001 HIS K 172 PHE 0.023 0.002 PHE K 24 TYR 0.023 0.001 TYR M 85 ARG 0.004 0.001 ARG M 40 ********************** 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 84 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 42 ILE cc_start: 0.9314 (tt) cc_final: 0.9105 (tt) REVERT: K 120 LYS cc_start: 0.8632 (tppt) cc_final: 0.7976 (ttpt) REVERT: K 148 TYR cc_start: 0.7769 (t80) cc_final: 0.7193 (t80) REVERT: L 55 GLN cc_start: 0.7811 (pp30) cc_final: 0.7586 (pp30) REVERT: M 82 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7471 (pp20) REVERT: M 119 GLU cc_start: 0.6822 (tp30) cc_final: 0.6445 (tp30) REVERT: M 157 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.6980 (mp) outliers start: 11 outliers final: 8 residues processed: 81 average time/residue: 0.2024 time to fit residues: 19.2964 Evaluate side-chains 80 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 157 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.137153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.118587 restraints weight = 8197.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.120202 restraints weight = 4006.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.121008 restraints weight = 2187.597| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4870 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= 0.186 Angle : 0.611 9.642 4674 Z= 0.334 Chirality : 0.040 0.139 508 Planarity : 0.005 0.040 603 Dihedral : 3.904 17.148 452 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.10 % Allowed : 24.23 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.42), residues: 413 helix: 2.67 (0.31), residues: 280 sheet: None (None), residues: 0 loop : -0.59 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 12 HIS 0.003 0.001 HIS K 122 PHE 0.015 0.001 PHE K 125 TYR 0.023 0.001 TYR M 85 ARG 0.004 0.001 ARG M 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1446.62 seconds wall clock time: 26 minutes 37.58 seconds (1597.58 seconds total)