Starting phenix.real_space_refine on Sun Mar 10 17:02:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9k_34570/03_2024/8h9k_34570.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9k_34570/03_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_34570/03_2024/8h9k_34570.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9k_34570/03_2024/8h9k_34570.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9k_34570/03_2024/8h9k_34570.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9k_34570/03_2024/8h9k_34570.pdb" } 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 Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 87": "OE1" <-> "OE2" Residue "K TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 137": "OE1" <-> "OE2" Residue "K GLU 150": "OE1" <-> "OE2" Residue "K TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 171": "OE1" <-> "OE2" Residue "L GLU 49": "OE1" <-> "OE2" Residue "L ASP 62": "OD1" <-> "OD2" Residue "L GLU 74": "OE1" <-> "OE2" Residue "M ASP 11": "OD1" <-> "OD2" Residue "M PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "M ASP 67": "OD1" <-> "OD2" Residue "M GLU 70": "OE1" <-> "OE2" Residue "M PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 93": "OE1" <-> "OE2" Residue "M GLU 115": "OE1" <-> "OE2" Residue "M GLU 117": "OE1" <-> "OE2" Residue "M GLU 119": "OE1" <-> "OE2" Residue "M PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 2.37, per 1000 atoms: 0.70 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 - 3.50 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: 1.36 Conformation dependent library (CDL) restraints added in 636.8 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: 0.27 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: 0.80 Time building geometry restraints manager: 1.48 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: 99.42 - 106.35: 100 106.35 - 113.28: 1859 113.28 - 120.21: 1343 120.21 - 127.13: 1335 127.13 - 134.06: 37 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 2.520 nonbonded pdb=" OG1 THR L 56 " pdb=" O GLY L 59 " model vdw 2.217 2.440 nonbonded pdb=" NE2 GLN K 162 " pdb=" O ASN M 59 " model vdw 2.217 2.520 nonbonded pdb=" NH1 ARG K 121 " pdb=" O ILE M 18 " model vdw 2.282 2.520 nonbonded pdb=" O GLU M 102 " pdb=" OG SER M 105 " model vdw 2.313 2.440 ... (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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.940 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: 27.010 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 13.940 Find NCS groups from input model: 0.080 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.930 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.376 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: 0.2179 time to fit residues: 30.3495 Evaluate side-chains 78 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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: 8.9990 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2843 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= 0.206 Angle : 0.602 4.797 4674 Z= 0.330 Chirality : 0.044 0.178 508 Planarity : 0.005 0.043 603 Dihedral : 5.257 56.316 452 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % 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: 0.48 (0.41), residues: 413 helix: 1.31 (0.29), residues: 290 sheet: None (None), residues: 0 loop : -2.14 (0.54), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 53 HIS 0.004 0.001 HIS K 103 PHE 0.010 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 fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7941 (mmmt) cc_final: 0.7565 (tptt) REVERT: K 118 VAL cc_start: 0.8296 (p) cc_final: 0.8011 (p) REVERT: K 143 ARG cc_start: 0.7213 (mtt180) cc_final: 0.6884 (mtm-85) REVERT: K 145 TYR cc_start: 0.7376 (t80) cc_final: 0.7081 (t80) REVERT: K 146 ARG cc_start: 0.7930 (ttm170) cc_final: 0.7435 (ttt180) REVERT: K 169 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7720 (tt0) REVERT: L 68 GLN cc_start: 0.7702 (tp-100) cc_final: 0.7295 (tp-100) REVERT: L 87 MET cc_start: 0.7786 (mpp) cc_final: 0.7045 (mpp) REVERT: M 118 MET cc_start: 0.7893 (tmm) cc_final: 0.7626 (tpp) outliers start: 15 outliers final: 12 residues processed: 99 average time/residue: 0.2041 time to fit residues: 23.3927 Evaluate side-chains 91 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 162 GLN 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: 0.8980 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3456 Z= 0.207 Angle : 0.565 6.155 4674 Z= 0.307 Chirality : 0.042 0.163 508 Planarity : 0.004 0.045 603 Dihedral : 5.052 56.472 452 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.51 % Allowed : 16.90 % Favored : 78.59 % 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: 1.41 (0.42), residues: 413 helix: 1.95 (0.29), residues: 291 sheet: None (None), residues: 0 loop : -1.67 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 103 HIS 0.007 0.001 HIS K 180 PHE 0.007 0.001 PHE L 100 TYR 0.010 0.001 TYR K 148 ARG 0.002 0.001 ARG K 154 *********************** 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: 16 poor density : 82 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7901 (mmmt) cc_final: 0.7526 (tptt) REVERT: K 85 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8011 (tt) REVERT: K 114 GLN cc_start: 0.8176 (mm110) cc_final: 0.7838 (mm-40) REVERT: K 118 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.7997 (p) REVERT: K 143 ARG cc_start: 0.7186 (mtt180) cc_final: 0.6840 (mtm-85) REVERT: K 145 TYR cc_start: 0.7564 (t80) cc_final: 0.7224 (t80) REVERT: K 146 ARG cc_start: 0.7949 (ttm170) cc_final: 0.7522 (ttt180) REVERT: K 150 GLU cc_start: 0.8363 (tt0) cc_final: 0.8106 (tt0) REVERT: L 77 LYS cc_start: 0.8813 (mmmm) cc_final: 0.8592 (mttt) REVERT: L 87 MET cc_start: 0.7789 (mpp) cc_final: 0.7470 (mmm) REVERT: M 94 LYS cc_start: 0.8730 (mttm) cc_final: 0.8423 (mttp) REVERT: M 118 MET cc_start: 0.7947 (tmm) cc_final: 0.7599 (tpp) outliers start: 16 outliers final: 11 residues processed: 94 average time/residue: 0.1942 time to fit residues: 21.2330 Evaluate side-chains 83 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 163 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3456 Z= 0.238 Angle : 0.593 9.306 4674 Z= 0.319 Chirality : 0.043 0.168 508 Planarity : 0.004 0.046 603 Dihedral : 5.127 60.031 452 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.23 % Allowed : 18.03 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.42), residues: 413 helix: 2.14 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -1.39 (0.58), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 53 HIS 0.003 0.001 HIS K 172 PHE 0.009 0.001 PHE K 58 TYR 0.008 0.001 TYR K 148 ARG 0.003 0.000 ARG K 154 *********************** 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 94 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7589 (tptm) REVERT: K 85 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8067 (tt) REVERT: K 114 GLN cc_start: 0.8177 (mm110) cc_final: 0.7869 (mm-40) REVERT: K 118 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.7809 (p) REVERT: K 143 ARG cc_start: 0.7242 (mtt180) cc_final: 0.6915 (mtm-85) REVERT: K 145 TYR cc_start: 0.7641 (t80) cc_final: 0.7295 (t80) REVERT: K 146 ARG cc_start: 0.7953 (ttm170) cc_final: 0.7506 (ttt180) REVERT: K 150 GLU cc_start: 0.8395 (tt0) cc_final: 0.8112 (tt0) REVERT: L 60 PRO cc_start: 0.6751 (Cg_endo) cc_final: 0.6479 (Cg_exo) REVERT: L 87 MET cc_start: 0.7852 (mpp) cc_final: 0.7557 (mmm) REVERT: M 19 ILE cc_start: 0.9004 (mm) cc_final: 0.8684 (tp) REVERT: M 94 LYS cc_start: 0.8755 (mttm) cc_final: 0.8464 (mttp) REVERT: M 118 MET cc_start: 0.8042 (tmm) cc_final: 0.7671 (tpp) outliers start: 15 outliers final: 11 residues processed: 90 average time/residue: 0.2075 time to fit residues: 21.7207 Evaluate side-chains 83 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3456 Z= 0.236 Angle : 0.606 7.879 4674 Z= 0.325 Chirality : 0.043 0.183 508 Planarity : 0.005 0.045 603 Dihedral : 5.199 62.254 452 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 6.20 % Allowed : 17.75 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.43), residues: 413 helix: 2.26 (0.29), residues: 289 sheet: None (None), residues: 0 loop : -1.00 (0.62), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 53 HIS 0.003 0.001 HIS K 172 PHE 0.009 0.001 PHE L 100 TYR 0.007 0.001 TYR K 148 ARG 0.006 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 99 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7592 (tptm) REVERT: K 85 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8074 (tt) REVERT: K 114 GLN cc_start: 0.8131 (mm110) cc_final: 0.7856 (mm-40) REVERT: K 118 VAL cc_start: 0.8217 (OUTLIER) cc_final: 0.7812 (p) REVERT: K 143 ARG cc_start: 0.7266 (mtt180) cc_final: 0.6932 (mtm-85) REVERT: K 145 TYR cc_start: 0.7656 (t80) cc_final: 0.7313 (t80) REVERT: K 146 ARG cc_start: 0.7951 (ttm170) cc_final: 0.7517 (ttt180) REVERT: K 150 GLU cc_start: 0.8389 (tt0) cc_final: 0.8120 (tt0) REVERT: L 60 PRO cc_start: 0.6586 (Cg_endo) cc_final: 0.6321 (Cg_exo) REVERT: L 68 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7987 (mm-40) REVERT: L 87 MET cc_start: 0.7873 (mpp) cc_final: 0.7613 (mmm) REVERT: M 19 ILE cc_start: 0.9015 (mm) cc_final: 0.8709 (tp) REVERT: M 94 LYS cc_start: 0.8759 (mttm) cc_final: 0.8464 (mttp) REVERT: M 118 MET cc_start: 0.8096 (tmm) cc_final: 0.7678 (tpp) outliers start: 22 outliers final: 15 residues processed: 92 average time/residue: 0.1970 time to fit residues: 21.2521 Evaluate side-chains 89 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 72 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 163 ASN Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 80 VAL 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: 0.8980 chunk 38 optimal weight: 0.0010 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4435 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= 0.166 Angle : 0.570 9.371 4674 Z= 0.305 Chirality : 0.041 0.176 508 Planarity : 0.004 0.043 603 Dihedral : 4.978 59.792 452 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.51 % Allowed : 20.00 % 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: 2.41 (0.43), residues: 413 helix: 2.55 (0.29), residues: 291 sheet: None (None), residues: 0 loop : -0.85 (0.63), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 53 HIS 0.002 0.001 HIS K 172 PHE 0.010 0.001 PHE L 100 TYR 0.011 0.001 TYR M 85 ARG 0.007 0.001 ARG K 167 *********************** 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 95 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7854 (mmmt) cc_final: 0.7513 (tptm) REVERT: K 114 GLN cc_start: 0.8042 (mm110) cc_final: 0.7832 (mm-40) REVERT: K 118 VAL cc_start: 0.8124 (OUTLIER) cc_final: 0.7609 (p) REVERT: K 129 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8759 (ptp-110) REVERT: K 134 MET cc_start: 0.8426 (ttm) cc_final: 0.7983 (ttm) REVERT: K 143 ARG cc_start: 0.7098 (mtt180) cc_final: 0.6786 (mtm-85) REVERT: K 145 TYR cc_start: 0.7658 (t80) cc_final: 0.7318 (t80) REVERT: K 146 ARG cc_start: 0.7920 (ttm170) cc_final: 0.7494 (ttt180) REVERT: K 150 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8119 (tt0) REVERT: K 163 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.7974 (t0) REVERT: L 60 PRO cc_start: 0.6444 (Cg_endo) cc_final: 0.6180 (Cg_exo) REVERT: L 68 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7767 (mm-40) REVERT: L 72 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7695 (mm-30) REVERT: L 87 MET cc_start: 0.7765 (mpp) cc_final: 0.7499 (mmm) REVERT: M 19 ILE cc_start: 0.8993 (mm) cc_final: 0.8739 (tp) REVERT: M 94 LYS cc_start: 0.8748 (mttm) cc_final: 0.8455 (mttp) REVERT: M 118 MET cc_start: 0.8124 (tmm) cc_final: 0.7721 (tpp) outliers start: 16 outliers final: 11 residues processed: 89 average time/residue: 0.2052 time to fit residues: 21.2816 Evaluate side-chains 85 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 129 ARG 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 10 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 180 HIS ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4573 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= 0.183 Angle : 0.600 10.916 4674 Z= 0.311 Chirality : 0.041 0.163 508 Planarity : 0.004 0.043 603 Dihedral : 4.899 59.195 452 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 5.35 % Allowed : 19.44 % 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: 2.64 (0.43), residues: 413 helix: 2.77 (0.29), residues: 284 sheet: None (None), residues: 0 loop : -0.67 (0.61), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 53 HIS 0.002 0.001 HIS K 172 PHE 0.010 0.001 PHE L 100 TYR 0.016 0.001 TYR K 148 ARG 0.004 0.001 ARG L 48 *********************** 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 94 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7879 (mmmt) cc_final: 0.7500 (tttm) REVERT: K 129 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8759 (ptp-110) REVERT: K 134 MET cc_start: 0.8411 (ttm) cc_final: 0.7955 (ttm) REVERT: K 143 ARG cc_start: 0.7109 (mtt180) cc_final: 0.6827 (mtm-85) REVERT: K 145 TYR cc_start: 0.7645 (t80) cc_final: 0.7329 (t80) REVERT: K 146 ARG cc_start: 0.7907 (ttm170) cc_final: 0.7519 (ttt180) REVERT: K 150 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8129 (tt0) REVERT: K 163 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.7924 (t0) REVERT: L 60 PRO cc_start: 0.6439 (Cg_endo) cc_final: 0.6184 (Cg_exo) REVERT: L 68 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7887 (mm-40) REVERT: L 87 MET cc_start: 0.7740 (mpp) cc_final: 0.7467 (mmm) REVERT: M 19 ILE cc_start: 0.9034 (mm) cc_final: 0.8787 (tp) REVERT: M 94 LYS cc_start: 0.8741 (mttm) cc_final: 0.8453 (mttp) REVERT: M 118 MET cc_start: 0.8137 (tmm) cc_final: 0.7724 (tpp) outliers start: 19 outliers final: 12 residues processed: 87 average time/residue: 0.2088 time to fit residues: 21.0378 Evaluate side-chains 84 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 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 L residue 103 ILE Chi-restraints excluded: chain M residue 10 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3456 Z= 0.193 Angle : 0.640 11.564 4674 Z= 0.324 Chirality : 0.042 0.173 508 Planarity : 0.004 0.042 603 Dihedral : 4.948 59.679 452 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.94 % Allowed : 21.69 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.42), residues: 413 helix: 2.76 (0.29), residues: 284 sheet: None (None), residues: 0 loop : -0.54 (0.61), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 53 HIS 0.002 0.001 HIS K 172 PHE 0.011 0.001 PHE L 100 TYR 0.013 0.001 TYR K 148 ARG 0.004 0.001 ARG K 167 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7875 (mmmt) cc_final: 0.7502 (tttm) REVERT: K 129 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8681 (ptp-110) REVERT: K 134 MET cc_start: 0.8407 (ttm) cc_final: 0.7944 (ttm) REVERT: K 143 ARG cc_start: 0.7110 (mtt180) cc_final: 0.6836 (mtm-85) REVERT: K 145 TYR cc_start: 0.7679 (t80) cc_final: 0.7369 (t80) REVERT: K 146 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7531 (ttt180) REVERT: K 150 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8102 (tt0) REVERT: K 163 ASN cc_start: 0.8518 (t0) cc_final: 0.7989 (t0) REVERT: K 164 MET cc_start: 0.6720 (tmm) cc_final: 0.5573 (tmm) REVERT: L 49 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7124 (mt-10) REVERT: L 60 PRO cc_start: 0.6443 (Cg_endo) cc_final: 0.6182 (Cg_exo) REVERT: L 68 GLN cc_start: 0.8237 (mm-40) cc_final: 0.8035 (mm-40) REVERT: L 75 LEU cc_start: 0.8415 (tp) cc_final: 0.8114 (tt) REVERT: L 87 MET cc_start: 0.7697 (mpp) cc_final: 0.7408 (mmm) REVERT: M 19 ILE cc_start: 0.9022 (mm) cc_final: 0.8800 (tp) REVERT: M 94 LYS cc_start: 0.8747 (mttm) cc_final: 0.8465 (mttp) REVERT: M 118 MET cc_start: 0.8140 (tmm) cc_final: 0.7724 (tpp) outliers start: 14 outliers final: 10 residues processed: 82 average time/residue: 0.2173 time to fit residues: 20.6043 Evaluate side-chains 80 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 97 ASP Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 10 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 0.0870 chunk 39 optimal weight: 0.0030 chunk 36 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.0060 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.0670 overall best weight: 0.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 3456 Z= 0.198 Angle : 0.634 12.766 4674 Z= 0.319 Chirality : 0.040 0.172 508 Planarity : 0.004 0.041 603 Dihedral : 4.656 53.070 452 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.54 % Allowed : 23.94 % 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: 2.92 (0.43), residues: 413 helix: 2.93 (0.30), residues: 285 sheet: None (None), residues: 0 loop : -0.45 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 12 HIS 0.002 0.000 HIS K 180 PHE 0.010 0.001 PHE K 21 TYR 0.014 0.001 TYR K 148 ARG 0.001 0.000 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7760 (mmmt) cc_final: 0.7459 (tptm) REVERT: K 134 MET cc_start: 0.8282 (ttm) cc_final: 0.7885 (ttm) REVERT: K 143 ARG cc_start: 0.7014 (mtt180) cc_final: 0.6639 (mtm-85) REVERT: K 145 TYR cc_start: 0.7650 (t80) cc_final: 0.7369 (t80) REVERT: K 146 ARG cc_start: 0.7885 (ttm170) cc_final: 0.7537 (ttt180) REVERT: K 150 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8034 (tt0) REVERT: K 163 ASN cc_start: 0.8438 (t0) cc_final: 0.7964 (t0) REVERT: K 164 MET cc_start: 0.6596 (tmm) cc_final: 0.6005 (tmm) REVERT: L 60 PRO cc_start: 0.6332 (Cg_endo) cc_final: 0.6090 (Cg_exo) REVERT: M 94 LYS cc_start: 0.8713 (mttm) cc_final: 0.8448 (mttp) REVERT: M 118 MET cc_start: 0.8145 (tmm) cc_final: 0.7740 (tpp) REVERT: M 130 MET cc_start: 0.7214 (ttt) cc_final: 0.7004 (ttp) outliers start: 9 outliers final: 6 residues processed: 81 average time/residue: 0.2169 time to fit residues: 20.4481 Evaluate side-chains 73 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 33 TRP 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: 0.9980 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 5 optimal weight: 0.0770 chunk 27 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 3456 Z= 0.223 Angle : 0.655 12.478 4674 Z= 0.329 Chirality : 0.041 0.195 508 Planarity : 0.004 0.042 603 Dihedral : 4.707 52.560 452 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.10 % Allowed : 23.38 % 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: 2.87 (0.43), residues: 413 helix: 2.88 (0.30), residues: 282 sheet: None (None), residues: 0 loop : -0.35 (0.59), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 33 HIS 0.005 0.001 HIS K 180 PHE 0.010 0.001 PHE L 100 TYR 0.012 0.001 TYR K 148 ARG 0.003 0.000 ARG K 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7806 (mmmt) cc_final: 0.7489 (tptm) REVERT: K 129 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8521 (ptp-110) REVERT: K 143 ARG cc_start: 0.7049 (mtt180) cc_final: 0.6666 (mtm-85) REVERT: K 145 TYR cc_start: 0.7670 (t80) cc_final: 0.7392 (t80) REVERT: K 146 ARG cc_start: 0.7892 (ttm170) cc_final: 0.7529 (ttt180) REVERT: K 150 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8102 (tt0) REVERT: K 163 ASN cc_start: 0.8433 (t0) cc_final: 0.7907 (t0) REVERT: K 164 MET cc_start: 0.6620 (tmm) cc_final: 0.6043 (tmm) REVERT: L 60 PRO cc_start: 0.6353 (Cg_endo) cc_final: 0.6106 (Cg_exo) REVERT: L 75 LEU cc_start: 0.8410 (tt) cc_final: 0.8184 (tp) REVERT: M 94 LYS cc_start: 0.8724 (mttm) cc_final: 0.8456 (mttp) REVERT: M 118 MET cc_start: 0.8105 (tmm) cc_final: 0.7667 (tpp) outliers start: 11 outliers final: 8 residues processed: 75 average time/residue: 0.2320 time to fit residues: 20.0010 Evaluate side-chains 73 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 33 TRP 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: 0.7980 chunk 36 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 0.0000 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 74 ASN ** 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 = 0.4024 r_free = 0.4024 target = 0.131020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.110484 restraints weight = 8889.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.112474 restraints weight = 4211.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.113657 restraints weight = 2468.557| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 3456 Z= 0.215 Angle : 0.640 13.060 4674 Z= 0.323 Chirality : 0.040 0.144 508 Planarity : 0.004 0.042 603 Dihedral : 4.689 50.670 452 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.25 % Allowed : 24.51 % Favored : 73.24 % 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: 2.76 (0.43), residues: 413 helix: 2.78 (0.30), residues: 284 sheet: None (None), residues: 0 loop : -0.40 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 12 HIS 0.005 0.001 HIS K 180 PHE 0.008 0.001 PHE K 21 TYR 0.012 0.001 TYR K 148 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: 1700.57 seconds wall clock time: 31 minutes 4.88 seconds (1864.88 seconds total)