Starting phenix.real_space_refine on Sun Mar 10 23:49:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4o_37267/03_2024/8w4o_37267_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4o_37267/03_2024/8w4o_37267.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4o_37267/03_2024/8w4o_37267_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4o_37267/03_2024/8w4o_37267_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4o_37267/03_2024/8w4o_37267_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4o_37267/03_2024/8w4o_37267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4o_37267/03_2024/8w4o_37267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4o_37267/03_2024/8w4o_37267_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4o_37267/03_2024/8w4o_37267_updated.pdb" } resolution = 3.23 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= -0.001 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 36 5.21 5 S 10 5.16 5 C 4356 2.51 5 N 763 2.21 5 O 878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "5 GLU 137": "OE1" <-> "OE2" 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: 6046 Number of models: 1 Model: "" Number of chains: 6 Chain: "5" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1280 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 156} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "7" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1222 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 9, 'TRANS': 154} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 45 Chain: "6" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1209 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 154} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 51 Chain: "5" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 914 Unusual residues: {'A86': 3, 'CLA': 11, 'ET4': 1, 'LHG': 3, 'LMG': 1, 'SQD': 1} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 284 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'CLA:plan-3': 2, 'CLA:plan-4': 5, 'CLA:plan-5': 7} Unresolved non-hydrogen planarities: 58 Chain: "7" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 707 Unusual residues: {'A86': 2, 'CLA': 12, 'DD6': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'CLA:plan-2': 1, 'CLA:plan-3': 4, 'CLA:plan-4': 7, 'CLA:plan-5': 10} Unresolved non-hydrogen planarities: 84 Chain: "6" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 714 Unusual residues: {'A86': 1, 'CLA': 13, 'DD6': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'CLA:plan-2': 3, 'CLA:plan-3': 3, 'CLA:plan-4': 6, 'CLA:plan-5': 11} Unresolved non-hydrogen planarities: 86 Time building chain proxies: 4.31, per 1000 atoms: 0.71 Number of scatterers: 6046 At special positions: 0 Unit cell: (80.56, 113.42, 66.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 P 3 15.00 Mg 36 11.99 O 878 8.00 N 763 7.00 C 4356 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=23, symmetry=0 Number of additional bonds: simple=23, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 734.5 milliseconds 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 890 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 0 sheets defined 51.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain '5' and resid 62 through 94 removed outlier: 3.589A pdb=" N SER 5 66 " --> pdb=" O PRO 5 62 " (cutoff:3.500A) Proline residue: 5 89 - end of helix Processing helix chain '5' and resid 109 through 111 No H-bonds generated for 'chain '5' and resid 109 through 111' Processing helix chain '5' and resid 117 through 137 Processing helix chain '5' and resid 159 through 188 Processing helix chain '5' and resid 193 through 201 removed outlier: 4.451A pdb=" N SER 5 200 " --> pdb=" O ASN 5 196 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY 5 201 " --> pdb=" O LEU 5 197 " (cutoff:3.500A) Processing helix chain '7' and resid 47 through 75 removed outlier: 4.460A pdb=" N ILE 7 72 " --> pdb=" O VAL 7 68 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA 7 73 " --> pdb=" O LEU 7 69 " (cutoff:3.500A) Proline residue: 7 74 - end of helix Processing helix chain '7' and resid 104 through 118 removed outlier: 3.638A pdb=" N LEU 7 113 " --> pdb=" O GLN 7 109 " (cutoff:3.500A) Processing helix chain '7' and resid 127 through 129 No H-bonds generated for 'chain '7' and resid 127 through 129' Processing helix chain '7' and resid 140 through 167 removed outlier: 3.649A pdb=" N LEU 7 153 " --> pdb=" O ARG 7 149 " (cutoff:3.500A) Processing helix chain '7' and resid 182 through 184 No H-bonds generated for 'chain '7' and resid 182 through 184' Processing helix chain '6' and resid 60 through 88 Proline residue: 6 87 - end of helix Processing helix chain '6' and resid 117 through 131 Processing helix chain '6' and resid 140 through 142 No H-bonds generated for 'chain '6' and resid 140 through 142' Processing helix chain '6' and resid 150 through 180 Processing helix chain '6' and resid 195 through 197 No H-bonds generated for 'chain '6' and resid 195 through 197' 186 hydrogen bonds defined for protein. 558 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: 1.37 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.35: 1498 1.35 - 1.54: 4642 1.54 - 1.72: 152 1.72 - 1.91: 17 1.91 - 2.09: 144 Bond restraints: 6453 Sorted by residual: bond pdb=" C27 DD6 6 204 " pdb=" C29 DD6 6 204 " ideal model delta sigma weight residual 1.545 1.242 0.303 2.00e-02 2.50e+03 2.29e+02 bond pdb=" C30 DD6 6 204 " pdb=" C31 DD6 6 204 " ideal model delta sigma weight residual 1.545 1.242 0.303 2.00e-02 2.50e+03 2.29e+02 bond pdb=" C30 DD6 7 304 " pdb=" C31 DD6 7 304 " ideal model delta sigma weight residual 1.545 1.252 0.293 2.00e-02 2.50e+03 2.14e+02 bond pdb=" C27 DD6 7 304 " pdb=" C29 DD6 7 304 " ideal model delta sigma weight residual 1.545 1.253 0.292 2.00e-02 2.50e+03 2.12e+02 bond pdb=" C31 DD6 6 204 " pdb=" C36 DD6 6 204 " ideal model delta sigma weight residual 1.612 1.322 0.290 2.00e-02 2.50e+03 2.10e+02 ... (remaining 6448 not shown) Histogram of bond angle deviations from ideal: 56.08 - 80.85: 30 80.85 - 105.62: 387 105.62 - 130.39: 8715 130.39 - 155.16: 210 155.16 - 179.93: 88 Bond angle restraints: 9430 Sorted by residual: angle pdb=" C28 DD6 6 204 " pdb=" C27 DD6 6 204 " pdb=" C29 DD6 6 204 " ideal model delta sigma weight residual 68.18 122.87 -54.69 3.00e+00 1.11e-01 3.32e+02 angle pdb=" C28 DD6 7 304 " pdb=" C27 DD6 7 304 " pdb=" C29 DD6 7 304 " ideal model delta sigma weight residual 68.18 121.01 -52.83 3.00e+00 1.11e-01 3.10e+02 angle pdb=" C08 ET4 5 302 " pdb=" C09 ET4 5 302 " pdb=" C27 ET4 5 302 " ideal model delta sigma weight residual 68.18 120.60 -52.42 3.00e+00 1.11e-01 3.05e+02 angle pdb=" C28 DD6 6 203 " pdb=" C27 DD6 6 203 " pdb=" C29 DD6 6 203 " ideal model delta sigma weight residual 68.18 119.49 -51.31 3.00e+00 1.11e-01 2.93e+02 angle pdb=" C28 DD6 7 303 " pdb=" C27 DD6 7 303 " pdb=" C29 DD6 7 303 " ideal model delta sigma weight residual 68.18 119.48 -51.30 3.00e+00 1.11e-01 2.92e+02 ... (remaining 9425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 2580 35.43 - 70.87: 225 70.87 - 106.30: 48 106.30 - 141.74: 20 141.74 - 177.17: 9 Dihedral angle restraints: 2882 sinusoidal: 1483 harmonic: 1399 Sorted by residual: dihedral pdb=" C34 A86 5 303 " pdb=" C38 A86 5 303 " pdb=" O4 A86 5 303 " pdb=" C39 A86 5 303 " ideal model delta sinusoidal sigma weight residual -177.27 -0.10 -177.17 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C34 A86 7 302 " pdb=" C38 A86 7 302 " pdb=" O4 A86 7 302 " pdb=" C39 A86 7 302 " ideal model delta sinusoidal sigma weight residual -177.27 -6.51 -170.76 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C15 DD6 7 304 " pdb=" C20 DD6 7 304 " pdb=" O1 DD6 7 304 " pdb=" C19 DD6 7 304 " ideal model delta sinusoidal sigma weight residual 79.23 -110.76 -170.01 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 2879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.005: 752 1.005 - 2.010: 9 2.010 - 3.015: 0 3.015 - 4.020: 0 4.020 - 5.025: 2 Chirality restraints: 763 Sorted by residual: chirality pdb=" C03 ET4 5 302 " pdb=" C02 ET4 5 302 " pdb=" C04 ET4 5 302 " pdb=" O31 ET4 5 302 " both_signs ideal model delta sigma weight residual False 2.50 -2.52 5.03 2.00e-01 2.50e+01 6.31e+02 chirality pdb=" C36 ET4 5 302 " pdb=" C35 ET4 5 302 " pdb=" C37 ET4 5 302 " pdb=" O40 ET4 5 302 " both_signs ideal model delta sigma weight residual False 2.48 -2.33 4.80 2.00e-01 2.50e+01 5.77e+02 chirality pdb=" C20 DD6 6 204 " pdb=" C15 DD6 6 204 " pdb=" C19 DD6 6 204 " pdb=" C21 DD6 6 204 " both_signs ideal model delta sigma weight residual True 2.74 0.86 1.87 2.00e-01 2.50e+01 8.78e+01 ... (remaining 760 not shown) Planarity restraints: 1276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 LHG 5 317 " 0.099 2.00e-02 2.50e+03 5.76e-02 3.31e+01 pdb=" C8 LHG 5 317 " -0.029 2.00e-02 2.50e+03 pdb=" O7 LHG 5 317 " -0.031 2.00e-02 2.50e+03 pdb=" O9 LHG 5 317 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 LHG 5 318 " 0.082 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C24 LHG 5 318 " -0.025 2.00e-02 2.50e+03 pdb=" O10 LHG 5 318 " -0.030 2.00e-02 2.50e+03 pdb=" O8 LHG 5 318 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 SQD 5 319 " -0.076 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C24 SQD 5 319 " 0.023 2.00e-02 2.50e+03 pdb=" O10 SQD 5 319 " 0.029 2.00e-02 2.50e+03 pdb=" O48 SQD 5 319 " 0.024 2.00e-02 2.50e+03 ... (remaining 1273 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 906 2.77 - 3.30: 5410 3.30 - 3.83: 10523 3.83 - 4.37: 11753 4.37 - 4.90: 19391 Nonbonded interactions: 47983 Sorted by model distance: nonbonded pdb=" O ASP 5 199 " pdb=" OG SER 5 200 " model vdw 2.237 2.440 nonbonded pdb=" OE2 GLU 6 70 " pdb=" NE ARG 6 162 " model vdw 2.268 2.520 nonbonded pdb=" OD2 ASP 7 37 " pdb=" OG SER 7 42 " model vdw 2.277 2.440 nonbonded pdb=" O ALA 5 125 " pdb=" OG SER 5 128 " model vdw 2.302 2.440 nonbonded pdb=" O PHE 6 184 " pdb=" O4 SQD 5 319 " model vdw 2.305 2.440 ... (remaining 47978 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 individual isotropic 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: 0.010 Normalize map: mean=0, sd=1: 5.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 27.190 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.310 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.020 0.303 6453 Z= 1.067 Angle : 3.284 54.694 9430 Z= 1.126 Chirality : 0.317 5.025 763 Planarity : 0.007 0.091 1276 Dihedral : 29.006 177.169 1992 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.85 % Favored : 85.95 % Rotamer: Outliers : 0.87 % Allowed : 0.87 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.53 (0.38), residues: 491 helix: 0.31 (0.32), residues: 263 sheet: None (None), residues: 0 loop : -4.38 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 6 92 HIS 0.004 0.001 HIS 7 60 PHE 0.013 0.001 PHE 6 136 TYR 0.010 0.001 TYR 6 84 ARG 0.003 0.001 ARG 6 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.436 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 87 average time/residue: 0.1380 time to fit residues: 16.7308 Evaluate side-chains 69 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.0270 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6453 Z= 0.218 Angle : 1.471 25.585 9430 Z= 0.524 Chirality : 0.082 0.931 763 Planarity : 0.006 0.072 1276 Dihedral : 26.808 177.238 1225 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.54 % Favored : 92.06 % Rotamer: Outliers : 2.02 % Allowed : 11.85 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.52 (0.38), residues: 491 helix: 0.98 (0.32), residues: 262 sheet: None (None), residues: 0 loop : -3.65 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 6 135 HIS 0.008 0.002 HIS 6 73 PHE 0.009 0.001 PHE 6 125 TYR 0.012 0.001 TYR 7 77 ARG 0.003 0.000 ARG 6 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.486 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 80 average time/residue: 0.1548 time to fit residues: 17.4381 Evaluate side-chains 71 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 7 residue 91 ASP Chi-restraints excluded: chain 7 residue 163 SER Chi-restraints excluded: chain 6 residue 109 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.0030 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6453 Z= 0.238 Angle : 1.393 24.614 9430 Z= 0.495 Chirality : 0.081 0.928 763 Planarity : 0.005 0.056 1276 Dihedral : 23.885 173.793 1225 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.76 % Favored : 91.04 % Rotamer: Outliers : 2.31 % Allowed : 13.58 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.88 (0.39), residues: 491 helix: 1.37 (0.31), residues: 265 sheet: None (None), residues: 0 loop : -3.23 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 6 135 HIS 0.008 0.002 HIS 6 73 PHE 0.010 0.001 PHE 6 125 TYR 0.016 0.001 TYR 5 94 ARG 0.004 0.001 ARG 6 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.505 Fit side-chains REVERT: 6 84 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.8136 (t80) REVERT: 6 168 ILE cc_start: 0.8868 (tp) cc_final: 0.8567 (tp) outliers start: 8 outliers final: 6 residues processed: 70 average time/residue: 0.1306 time to fit residues: 13.3187 Evaluate side-chains 67 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 7 residue 68 VAL Chi-restraints excluded: chain 7 residue 163 SER Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 0.0470 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6453 Z= 0.211 Angle : 1.339 24.220 9430 Z= 0.475 Chirality : 0.081 0.942 763 Planarity : 0.005 0.047 1276 Dihedral : 22.575 174.947 1225 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.92 % Favored : 92.87 % Rotamer: Outliers : 2.89 % Allowed : 15.90 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.39 (0.40), residues: 491 helix: 1.72 (0.31), residues: 265 sheet: None (None), residues: 0 loop : -2.93 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 6 92 HIS 0.007 0.002 HIS 6 73 PHE 0.008 0.001 PHE 6 125 TYR 0.010 0.001 TYR 7 90 ARG 0.003 0.000 ARG 6 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.503 Fit side-chains REVERT: 7 125 ASP cc_start: 0.8475 (t0) cc_final: 0.8257 (t0) REVERT: 6 84 TYR cc_start: 0.9075 (OUTLIER) cc_final: 0.8203 (t80) REVERT: 6 168 ILE cc_start: 0.8910 (tp) cc_final: 0.8583 (tp) REVERT: 6 189 ASN cc_start: 0.8884 (m-40) cc_final: 0.8665 (m-40) outliers start: 10 outliers final: 7 residues processed: 73 average time/residue: 0.1370 time to fit residues: 14.2066 Evaluate side-chains 74 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 7 residue 68 VAL Chi-restraints excluded: chain 7 residue 91 ASP Chi-restraints excluded: chain 7 residue 163 SER Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 11 optimal weight: 0.0970 chunk 15 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6453 Z= 0.199 Angle : 1.295 23.835 9430 Z= 0.460 Chirality : 0.081 0.934 763 Planarity : 0.005 0.042 1276 Dihedral : 22.038 175.608 1225 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.74 % Favored : 92.06 % Rotamer: Outliers : 3.47 % Allowed : 16.18 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.20 (0.40), residues: 491 helix: 1.88 (0.31), residues: 265 sheet: None (None), residues: 0 loop : -2.83 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 6 92 HIS 0.007 0.002 HIS 6 73 PHE 0.009 0.001 PHE 6 125 TYR 0.010 0.001 TYR 7 77 ARG 0.004 0.000 ARG 6 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.465 Fit side-chains REVERT: 5 149 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8148 (mm-30) REVERT: 7 125 ASP cc_start: 0.8472 (t0) cc_final: 0.8240 (t0) REVERT: 6 84 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.8193 (t80) REVERT: 6 168 ILE cc_start: 0.8886 (tp) cc_final: 0.8562 (tp) REVERT: 6 189 ASN cc_start: 0.8932 (m-40) cc_final: 0.8697 (m-40) outliers start: 12 outliers final: 9 residues processed: 74 average time/residue: 0.1236 time to fit residues: 13.5467 Evaluate side-chains 69 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 7 residue 91 ASP Chi-restraints excluded: chain 7 residue 163 SER Chi-restraints excluded: chain 6 residue 40 LEU Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 138 ASN Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.2980 chunk 46 optimal weight: 0.2980 chunk 38 optimal weight: 0.0870 chunk 21 optimal weight: 0.0770 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.1654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6453 Z= 0.139 Angle : 1.265 23.715 9430 Z= 0.448 Chirality : 0.081 0.946 763 Planarity : 0.004 0.043 1276 Dihedral : 21.426 175.677 1225 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.92 % Favored : 92.87 % Rotamer: Outliers : 2.31 % Allowed : 17.92 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.05 (0.40), residues: 491 helix: 2.08 (0.31), residues: 265 sheet: None (None), residues: 0 loop : -2.71 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP 6 135 HIS 0.005 0.001 HIS 6 73 PHE 0.006 0.001 PHE 6 94 TYR 0.017 0.001 TYR 5 94 ARG 0.004 0.000 ARG 6 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.524 Fit side-chains REVERT: 5 131 GLU cc_start: 0.8271 (tt0) cc_final: 0.7925 (tt0) REVERT: 5 177 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8204 (mm) REVERT: 7 125 ASP cc_start: 0.8423 (t0) cc_final: 0.8189 (t0) REVERT: 6 84 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.8364 (t80) REVERT: 6 168 ILE cc_start: 0.8879 (tp) cc_final: 0.8602 (tp) outliers start: 8 outliers final: 3 residues processed: 80 average time/residue: 0.1366 time to fit residues: 15.6252 Evaluate side-chains 74 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 177 LEU Chi-restraints excluded: chain 7 residue 91 ASP Chi-restraints excluded: chain 6 residue 40 LEU Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 141 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 189 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6453 Z= 0.322 Angle : 1.270 24.217 9430 Z= 0.458 Chirality : 0.081 0.922 763 Planarity : 0.005 0.042 1276 Dihedral : 21.361 175.923 1225 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.35 % Favored : 91.45 % Rotamer: Outliers : 3.47 % Allowed : 18.21 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.19 (0.40), residues: 491 helix: 1.83 (0.31), residues: 265 sheet: None (None), residues: 0 loop : -2.75 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 6 120 HIS 0.009 0.003 HIS 6 73 PHE 0.012 0.001 PHE 6 125 TYR 0.016 0.002 TYR 5 94 ARG 0.004 0.001 ARG 5 173 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.517 Fit side-chains REVERT: 7 71 TYR cc_start: 0.9176 (OUTLIER) cc_final: 0.8929 (m-80) REVERT: 7 125 ASP cc_start: 0.8492 (t0) cc_final: 0.8270 (t0) REVERT: 6 84 TYR cc_start: 0.9164 (OUTLIER) cc_final: 0.8178 (t80) REVERT: 6 168 ILE cc_start: 0.8942 (tp) cc_final: 0.8654 (tp) outliers start: 12 outliers final: 8 residues processed: 71 average time/residue: 0.1372 time to fit residues: 14.0654 Evaluate side-chains 70 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 7 residue 71 TYR Chi-restraints excluded: chain 7 residue 91 ASP Chi-restraints excluded: chain 6 residue 40 LEU Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 176 SER Chi-restraints excluded: chain 6 residue 189 ASN Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 189 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6453 Z= 0.285 Angle : 1.257 24.120 9430 Z= 0.453 Chirality : 0.082 0.933 763 Planarity : 0.005 0.043 1276 Dihedral : 21.145 175.840 1225 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.15 % Favored : 91.65 % Rotamer: Outliers : 4.34 % Allowed : 19.08 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.25 (0.39), residues: 491 helix: 1.77 (0.31), residues: 264 sheet: None (None), residues: 0 loop : -2.74 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 6 92 HIS 0.009 0.003 HIS 7 60 PHE 0.011 0.001 PHE 7 155 TYR 0.014 0.001 TYR 5 94 ARG 0.003 0.000 ARG 5 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 0.478 Fit side-chains REVERT: 7 71 TYR cc_start: 0.9140 (OUTLIER) cc_final: 0.8851 (m-80) REVERT: 7 125 ASP cc_start: 0.8486 (t0) cc_final: 0.8255 (t0) REVERT: 6 84 TYR cc_start: 0.9147 (OUTLIER) cc_final: 0.8122 (t80) REVERT: 6 168 ILE cc_start: 0.8931 (tp) cc_final: 0.8651 (tp) outliers start: 15 outliers final: 10 residues processed: 73 average time/residue: 0.1261 time to fit residues: 13.4129 Evaluate side-chains 72 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 7 residue 71 TYR Chi-restraints excluded: chain 7 residue 91 ASP Chi-restraints excluded: chain 7 residue 163 SER Chi-restraints excluded: chain 6 residue 40 LEU Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 176 SER Chi-restraints excluded: chain 6 residue 189 ASN Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.0670 chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 114 ASN ** 7 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 189 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6453 Z= 0.194 Angle : 1.235 23.726 9430 Z= 0.444 Chirality : 0.081 0.941 763 Planarity : 0.005 0.043 1276 Dihedral : 21.039 176.014 1225 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.74 % Favored : 92.06 % Rotamer: Outliers : 2.89 % Allowed : 21.10 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.14 (0.40), residues: 491 helix: 1.84 (0.31), residues: 264 sheet: None (None), residues: 0 loop : -2.66 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP 6 92 HIS 0.007 0.003 HIS 7 60 PHE 0.010 0.001 PHE 7 155 TYR 0.012 0.001 TYR 5 94 ARG 0.003 0.000 ARG 6 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.475 Fit side-chains REVERT: 7 71 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.8883 (m-80) REVERT: 7 125 ASP cc_start: 0.8467 (t0) cc_final: 0.8236 (t0) REVERT: 6 84 TYR cc_start: 0.9094 (OUTLIER) cc_final: 0.8101 (t80) REVERT: 6 168 ILE cc_start: 0.8923 (tp) cc_final: 0.8656 (tp) outliers start: 10 outliers final: 7 residues processed: 71 average time/residue: 0.1195 time to fit residues: 12.5541 Evaluate side-chains 69 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 7 residue 71 TYR Chi-restraints excluded: chain 7 residue 91 ASP Chi-restraints excluded: chain 7 residue 163 SER Chi-restraints excluded: chain 6 residue 40 LEU Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 138 ASN Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 0.0980 chunk 23 optimal weight: 0.4980 chunk 30 optimal weight: 0.1980 chunk 40 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 114 ASN ** 7 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6453 Z= 0.194 Angle : 1.235 23.726 9430 Z= 0.444 Chirality : 0.081 0.941 763 Planarity : 0.005 0.043 1276 Dihedral : 21.039 176.014 1225 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.74 % Favored : 92.06 % Rotamer: Outliers : 2.60 % Allowed : 21.39 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.14 (0.40), residues: 491 helix: 1.84 (0.31), residues: 264 sheet: None (None), residues: 0 loop : -2.66 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP 6 92 HIS 0.007 0.003 HIS 7 60 PHE 0.010 0.001 PHE 7 155 TYR 0.012 0.001 TYR 5 94 ARG 0.003 0.000 ARG 6 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.480 Fit side-chains REVERT: 7 71 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.8883 (m-80) REVERT: 7 125 ASP cc_start: 0.8467 (t0) cc_final: 0.8236 (t0) REVERT: 6 84 TYR cc_start: 0.9088 (OUTLIER) cc_final: 0.8101 (t80) REVERT: 6 168 ILE cc_start: 0.8923 (tp) cc_final: 0.8656 (tp) outliers start: 9 outliers final: 7 residues processed: 66 average time/residue: 0.1121 time to fit residues: 11.1452 Evaluate side-chains 69 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 7 residue 71 TYR Chi-restraints excluded: chain 7 residue 91 ASP Chi-restraints excluded: chain 7 residue 163 SER Chi-restraints excluded: chain 6 residue 40 LEU Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 138 ASN Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 39 optimal weight: 0.0170 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.0040 overall best weight: 0.4030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 114 ASN 7 146 GLN 6 189 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.077737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.066473 restraints weight = 13480.443| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.95 r_work: 0.2664 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6453 Z= 0.180 Angle : 1.218 23.157 9430 Z= 0.437 Chirality : 0.081 0.941 763 Planarity : 0.005 0.044 1276 Dihedral : 20.723 175.961 1225 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.35 % Favored : 91.45 % Rotamer: Outliers : 3.47 % Allowed : 20.52 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.01 (0.40), residues: 491 helix: 1.93 (0.31), residues: 265 sheet: None (None), residues: 0 loop : -2.59 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP 6 92 HIS 0.007 0.002 HIS 7 60 PHE 0.008 0.001 PHE 7 155 TYR 0.012 0.001 TYR 5 94 ARG 0.003 0.000 ARG 6 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1816.04 seconds wall clock time: 33 minutes 35.23 seconds (2015.23 seconds total)