Starting phenix.real_space_refine on Tue Feb 13 16:59:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aw5_15691/02_2024/8aw5_15691_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aw5_15691/02_2024/8aw5_15691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aw5_15691/02_2024/8aw5_15691.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aw5_15691/02_2024/8aw5_15691.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aw5_15691/02_2024/8aw5_15691_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aw5_15691/02_2024/8aw5_15691_updated.pdb" } resolution = 2.8 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= 0.004 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 Fe 3 7.16 5 P 9 5.49 5 S 21 5.16 5 C 4887 2.51 5 N 975 2.21 5 O 1128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 137": "NH1" <-> "NH2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C ARG 172": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7023 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2142 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 9, 'TRANS': 256} Chain breaks: 1 Chain: "B" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2142 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 9, 'TRANS': 256} Chain breaks: 1 Chain: "C" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2142 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 9, 'TRANS': 256} Chain breaks: 1 Chain: "A" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 199 Unusual residues: {'HEM': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 199 Unusual residues: {'HEM': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 199 Unusual residues: {'HEM': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.40, per 1000 atoms: 0.63 Number of scatterers: 7023 At special positions: 0 Unit cell: (88.56, 93.48, 72.57, 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) Fe 3 26.01 S 21 16.00 P 9 15.00 O 1128 8.00 N 975 7.00 C 4887 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.1 seconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 0 sheets defined 76.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 11 through 32 Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 75 through 100 removed outlier: 3.693A pdb=" N PHE A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 125 Processing helix chain 'A' and resid 134 through 166 removed outlier: 3.642A pdb=" N LEU A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 199 Processing helix chain 'A' and resid 204 through 230 removed outlier: 4.082A pdb=" N GLY A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 255 Processing helix chain 'A' and resid 260 through 288 Proline residue: A 283 - end of helix removed outlier: 4.594A pdb=" N THR A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 32 Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 75 through 100 removed outlier: 3.694A pdb=" N PHE B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 125 Processing helix chain 'B' and resid 134 through 166 removed outlier: 3.643A pdb=" N LEU B 149 " --> pdb=" O THR B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 199 Processing helix chain 'B' and resid 204 through 230 removed outlier: 4.081A pdb=" N GLY B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 255 Processing helix chain 'B' and resid 260 through 288 Proline residue: B 283 - end of helix removed outlier: 4.594A pdb=" N THR B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 32 Processing helix chain 'C' and resid 53 through 55 No H-bonds generated for 'chain 'C' and resid 53 through 55' Processing helix chain 'C' and resid 75 through 100 removed outlier: 3.694A pdb=" N PHE C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 125 Processing helix chain 'C' and resid 134 through 166 removed outlier: 3.642A pdb=" N LEU C 149 " --> pdb=" O THR C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 199 Processing helix chain 'C' and resid 204 through 230 removed outlier: 4.081A pdb=" N GLY C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE C 219 " --> pdb=" O THR C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 255 Processing helix chain 'C' and resid 260 through 288 Proline residue: C 283 - end of helix removed outlier: 4.594A pdb=" N THR C 288 " --> pdb=" O SER C 284 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1440 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: 1.98 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 2444 1.38 - 1.55: 4708 1.55 - 1.72: 21 1.72 - 1.89: 36 1.89 - 2.06: 12 Bond restraints: 7221 Sorted by residual: bond pdb=" C21 POV C 404 " pdb=" O22 POV C 404 " ideal model delta sigma weight residual 1.205 1.438 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C21 POV A 402 " pdb=" O22 POV A 402 " ideal model delta sigma weight residual 1.205 1.438 -0.233 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C21 POV B 402 " pdb=" O22 POV B 402 " ideal model delta sigma weight residual 1.205 1.438 -0.233 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C21 POV A 404 " pdb=" O22 POV A 404 " ideal model delta sigma weight residual 1.205 1.434 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C21 POV A 403 " pdb=" O22 POV A 403 " ideal model delta sigma weight residual 1.205 1.434 -0.229 2.00e-02 2.50e+03 1.31e+02 ... (remaining 7216 not shown) Histogram of bond angle deviations from ideal: 88.19 - 105.61: 156 105.61 - 123.04: 9117 123.04 - 140.46: 513 140.46 - 157.89: 0 157.89 - 175.32: 6 Bond angle restraints: 9792 Sorted by residual: angle pdb=" N GLU C 204 " pdb=" CA GLU C 204 " pdb=" C GLU C 204 " ideal model delta sigma weight residual 111.69 99.00 12.69 1.23e+00 6.61e-01 1.07e+02 angle pdb=" N GLU A 204 " pdb=" CA GLU A 204 " pdb=" C GLU A 204 " ideal model delta sigma weight residual 111.69 99.01 12.68 1.23e+00 6.61e-01 1.06e+02 angle pdb=" N GLU B 204 " pdb=" CA GLU B 204 " pdb=" C GLU B 204 " ideal model delta sigma weight residual 112.45 98.98 13.47 1.39e+00 5.18e-01 9.39e+01 angle pdb=" N VAL C 32 " pdb=" CA VAL C 32 " pdb=" C VAL C 32 " ideal model delta sigma weight residual 111.45 103.72 7.73 9.30e-01 1.16e+00 6.92e+01 angle pdb=" N VAL B 32 " pdb=" CA VAL B 32 " pdb=" C VAL B 32 " ideal model delta sigma weight residual 111.45 103.73 7.72 9.30e-01 1.16e+00 6.89e+01 ... (remaining 9787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.36: 3951 28.36 - 56.72: 150 56.72 - 85.07: 45 85.07 - 113.43: 18 113.43 - 141.79: 6 Dihedral angle restraints: 4170 sinusoidal: 1827 harmonic: 2343 Sorted by residual: dihedral pdb=" C3 POV C 404 " pdb=" C31 POV C 404 " pdb=" O31 POV C 404 " pdb=" C32 POV C 404 " ideal model delta sinusoidal sigma weight residual 172.61 -45.60 -141.79 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" C3 POV A 402 " pdb=" C31 POV A 402 " pdb=" O31 POV A 402 " pdb=" C32 POV A 402 " ideal model delta sinusoidal sigma weight residual 172.61 -45.64 -141.75 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" C3 POV B 402 " pdb=" C31 POV B 402 " pdb=" O31 POV B 402 " pdb=" C32 POV B 402 " ideal model delta sinusoidal sigma weight residual 172.61 -45.67 -141.72 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 4167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 779 0.062 - 0.123: 235 0.123 - 0.185: 65 0.185 - 0.247: 10 0.247 - 0.309: 12 Chirality restraints: 1101 Sorted by residual: chirality pdb=" CA GLU A 204 " pdb=" N GLU A 204 " pdb=" C GLU A 204 " pdb=" CB GLU A 204 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA GLU B 204 " pdb=" N GLU B 204 " pdb=" C GLU B 204 " pdb=" CB GLU B 204 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA GLU C 204 " pdb=" N GLU C 204 " pdb=" C GLU C 204 " pdb=" CB GLU C 204 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 1098 not shown) Planarity restraints: 1095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV C 402 " -0.151 2.00e-02 2.50e+03 2.72e-01 7.38e+02 pdb=" C29 POV C 402 " 0.352 2.00e-02 2.50e+03 pdb="C210 POV C 402 " -0.354 2.00e-02 2.50e+03 pdb="C211 POV C 402 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 403 " -0.151 2.00e-02 2.50e+03 2.72e-01 7.37e+02 pdb=" C29 POV A 403 " 0.352 2.00e-02 2.50e+03 pdb="C210 POV A 403 " -0.354 2.00e-02 2.50e+03 pdb="C211 POV A 403 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B 403 " 0.150 2.00e-02 2.50e+03 2.72e-01 7.37e+02 pdb=" C29 POV B 403 " -0.352 2.00e-02 2.50e+03 pdb="C210 POV B 403 " 0.354 2.00e-02 2.50e+03 pdb="C211 POV B 403 " -0.152 2.00e-02 2.50e+03 ... (remaining 1092 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 2874 2.92 - 3.42: 7667 3.42 - 3.91: 12276 3.91 - 4.41: 13979 4.41 - 4.90: 22748 Nonbonded interactions: 59544 Sorted by model distance: nonbonded pdb=" OG SER A 157 " pdb=" OH TYR A 184 " model vdw 2.427 2.440 nonbonded pdb=" OG SER B 157 " pdb=" OH TYR B 184 " model vdw 2.427 2.440 nonbonded pdb=" OG SER C 157 " pdb=" OH TYR C 184 " model vdw 2.428 2.440 nonbonded pdb=" O GLY B 29 " pdb=" OG1 THR B 33 " model vdw 2.446 2.440 nonbonded pdb=" O GLY A 29 " pdb=" OG1 THR A 33 " model vdw 2.446 2.440 ... (remaining 59539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 3.720 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.780 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 0.017 0.233 7221 Z= 1.045 Angle : 1.758 17.246 9792 Z= 0.905 Chirality : 0.070 0.309 1101 Planarity : 0.036 0.272 1095 Dihedral : 18.375 141.787 2676 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.58 % Favored : 95.04 % Rotamer: Outliers : 0.43 % Allowed : 6.06 % Favored : 93.51 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.31), residues: 786 helix: 1.25 (0.21), residues: 621 sheet: None (None), residues: 0 loop : -3.62 (0.42), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 276 HIS 0.002 0.001 HIS C 81 PHE 0.014 0.002 PHE A 272 TYR 0.010 0.001 TYR B 164 ARG 0.002 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 178 time to evaluate : 0.791 Fit side-chains REVERT: A 14 LEU cc_start: 0.8819 (mt) cc_final: 0.8500 (mt) REVERT: A 171 GLU cc_start: 0.8036 (mp0) cc_final: 0.7750 (mp0) REVERT: B 143 VAL cc_start: 0.8928 (t) cc_final: 0.8700 (t) REVERT: B 203 LEU cc_start: 0.8183 (tp) cc_final: 0.7942 (tp) REVERT: B 246 GLN cc_start: 0.9056 (tp40) cc_final: 0.8711 (tp40) REVERT: C 243 MET cc_start: 0.8768 (mmt) cc_final: 0.8409 (mmt) outliers start: 3 outliers final: 0 residues processed: 178 average time/residue: 1.1080 time to fit residues: 208.2469 Evaluate side-chains 105 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.0870 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 HIS B 141 HIS C 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7221 Z= 0.243 Angle : 0.623 9.996 9792 Z= 0.281 Chirality : 0.038 0.146 1101 Planarity : 0.003 0.027 1095 Dihedral : 19.508 131.028 1278 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.75 % Allowed : 15.30 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.31 (0.30), residues: 786 helix: 2.50 (0.20), residues: 627 sheet: None (None), residues: 0 loop : -2.73 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 44 HIS 0.004 0.001 HIS B 213 PHE 0.015 0.002 PHE C 272 TYR 0.015 0.001 TYR C 199 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 0.777 Fit side-chains REVERT: A 14 LEU cc_start: 0.8743 (mt) cc_final: 0.8482 (mt) REVERT: A 78 GLU cc_start: 0.7470 (tp30) cc_final: 0.7264 (tp30) REVERT: A 171 GLU cc_start: 0.7886 (mp0) cc_final: 0.7634 (mp0) REVERT: A 172 ARG cc_start: 0.6377 (tpm170) cc_final: 0.5993 (tpp-160) REVERT: A 201 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7733 (mmtm) REVERT: B 78 GLU cc_start: 0.7367 (tp30) cc_final: 0.7163 (tp30) REVERT: B 172 ARG cc_start: 0.6334 (tpm170) cc_final: 0.6006 (tpp-160) REVERT: C 243 MET cc_start: 0.8899 (mmt) cc_final: 0.8525 (mmt) outliers start: 26 outliers final: 9 residues processed: 121 average time/residue: 1.4167 time to fit residues: 179.3616 Evaluate side-chains 101 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 181 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 48 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 141 HIS C 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7221 Z= 0.257 Angle : 0.603 9.076 9792 Z= 0.277 Chirality : 0.038 0.141 1101 Planarity : 0.003 0.029 1095 Dihedral : 18.704 126.403 1278 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.18 % Allowed : 15.01 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.79 (0.30), residues: 786 helix: 2.89 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -2.70 (0.43), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 44 HIS 0.004 0.001 HIS A 266 PHE 0.016 0.002 PHE B 272 TYR 0.014 0.001 TYR C 199 ARG 0.002 0.000 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 104 time to evaluate : 0.785 Fit side-chains REVERT: A 14 LEU cc_start: 0.8668 (mt) cc_final: 0.8378 (mt) REVERT: A 201 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7732 (mmtm) REVERT: B 143 VAL cc_start: 0.9092 (t) cc_final: 0.8876 (t) REVERT: B 172 ARG cc_start: 0.6558 (tpm170) cc_final: 0.6276 (tpp-160) REVERT: B 234 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8285 (ptmm) REVERT: C 139 LEU cc_start: 0.8080 (tt) cc_final: 0.7869 (tm) REVERT: C 243 MET cc_start: 0.8877 (mmt) cc_final: 0.8638 (mmt) outliers start: 29 outliers final: 13 residues processed: 121 average time/residue: 1.4071 time to fit residues: 178.3064 Evaluate side-chains 111 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TRP Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 181 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7221 Z= 0.260 Angle : 0.602 8.209 9792 Z= 0.276 Chirality : 0.038 0.131 1101 Planarity : 0.003 0.030 1095 Dihedral : 18.422 130.160 1278 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.75 % Allowed : 16.45 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.86 (0.30), residues: 786 helix: 2.90 (0.20), residues: 627 sheet: None (None), residues: 0 loop : -2.64 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 276 HIS 0.003 0.001 HIS A 266 PHE 0.016 0.002 PHE C 115 TYR 0.013 0.001 TYR C 199 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 0.712 Fit side-chains REVERT: A 14 LEU cc_start: 0.8671 (mt) cc_final: 0.8383 (mt) REVERT: A 201 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7730 (mmtm) REVERT: B 143 VAL cc_start: 0.9100 (t) cc_final: 0.8880 (t) REVERT: B 172 ARG cc_start: 0.6527 (tpm170) cc_final: 0.6010 (mmp80) REVERT: B 175 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6563 (mm-30) REVERT: B 234 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8326 (ptmm) REVERT: C 78 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7258 (tp30) REVERT: C 139 LEU cc_start: 0.8072 (tt) cc_final: 0.7838 (tm) REVERT: C 243 MET cc_start: 0.8875 (mmt) cc_final: 0.8595 (mmt) outliers start: 26 outliers final: 12 residues processed: 113 average time/residue: 1.4799 time to fit residues: 175.1211 Evaluate side-chains 110 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 141 HIS C 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7221 Z= 0.333 Angle : 0.643 8.900 9792 Z= 0.295 Chirality : 0.040 0.142 1101 Planarity : 0.004 0.033 1095 Dihedral : 18.696 140.620 1278 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.46 % Allowed : 16.88 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.62 (0.30), residues: 786 helix: 2.74 (0.20), residues: 627 sheet: None (None), residues: 0 loop : -2.72 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 276 HIS 0.003 0.001 HIS A 266 PHE 0.019 0.002 PHE C 115 TYR 0.014 0.001 TYR C 199 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 0.807 Fit side-chains REVERT: A 201 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7753 (mmtm) REVERT: B 172 ARG cc_start: 0.6654 (tpm170) cc_final: 0.6127 (mmp80) REVERT: B 234 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8403 (ptmm) REVERT: C 78 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7241 (tp30) REVERT: C 243 MET cc_start: 0.8850 (mmt) cc_final: 0.8515 (mmt) outliers start: 24 outliers final: 13 residues processed: 108 average time/residue: 1.5046 time to fit residues: 169.6783 Evaluate side-chains 108 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 181 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 75 optimal weight: 0.0980 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 141 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7221 Z= 0.224 Angle : 0.573 8.000 9792 Z= 0.264 Chirality : 0.037 0.125 1101 Planarity : 0.003 0.032 1095 Dihedral : 17.954 134.740 1278 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.54 % Favored : 97.33 % Rotamer: Outliers : 3.46 % Allowed : 17.75 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.30), residues: 786 helix: 2.91 (0.20), residues: 627 sheet: None (None), residues: 0 loop : -2.61 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 276 HIS 0.003 0.001 HIS B 213 PHE 0.014 0.002 PHE C 272 TYR 0.014 0.001 TYR C 199 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 0.782 Fit side-chains REVERT: A 14 LEU cc_start: 0.8688 (mt) cc_final: 0.8399 (mt) REVERT: B 172 ARG cc_start: 0.6613 (tpm170) cc_final: 0.6120 (mmp80) REVERT: B 234 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8294 (ptmm) REVERT: C 78 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7189 (tp30) REVERT: C 243 MET cc_start: 0.8888 (mmt) cc_final: 0.8630 (mmt) outliers start: 24 outliers final: 9 residues processed: 115 average time/residue: 1.4353 time to fit residues: 172.4877 Evaluate side-chains 107 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 140 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7221 Z= 0.241 Angle : 0.598 9.205 9792 Z= 0.274 Chirality : 0.038 0.127 1101 Planarity : 0.003 0.032 1095 Dihedral : 17.740 131.644 1278 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.67 % Favored : 96.95 % Rotamer: Outliers : 2.89 % Allowed : 19.05 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.83 (0.30), residues: 786 helix: 2.89 (0.20), residues: 627 sheet: None (None), residues: 0 loop : -2.69 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.003 0.001 HIS A 266 PHE 0.015 0.002 PHE C 115 TYR 0.014 0.001 TYR C 199 ARG 0.001 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 0.751 Fit side-chains REVERT: A 14 LEU cc_start: 0.8673 (mt) cc_final: 0.8377 (mt) REVERT: A 201 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7784 (mmtm) REVERT: B 172 ARG cc_start: 0.6669 (tpm170) cc_final: 0.6194 (mmp80) REVERT: B 234 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8330 (ptmm) REVERT: C 78 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7185 (tp30) REVERT: C 243 MET cc_start: 0.8888 (mmt) cc_final: 0.8625 (mmt) outliers start: 20 outliers final: 13 residues processed: 113 average time/residue: 1.4789 time to fit residues: 174.5857 Evaluate side-chains 112 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 260 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 0.0050 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN C 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7221 Z= 0.209 Angle : 0.567 8.187 9792 Z= 0.263 Chirality : 0.037 0.123 1101 Planarity : 0.003 0.032 1095 Dihedral : 17.253 123.946 1278 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.42 % Favored : 97.20 % Rotamer: Outliers : 2.89 % Allowed : 18.76 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.94 (0.30), residues: 786 helix: 2.96 (0.20), residues: 627 sheet: None (None), residues: 0 loop : -2.62 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 276 HIS 0.002 0.001 HIS C 213 PHE 0.014 0.001 PHE C 115 TYR 0.012 0.001 TYR C 199 ARG 0.001 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 0.796 Fit side-chains REVERT: A 14 LEU cc_start: 0.8665 (mt) cc_final: 0.8383 (mt) REVERT: B 172 ARG cc_start: 0.6666 (tpm170) cc_final: 0.6232 (mmp80) REVERT: B 234 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8315 (ptmm) REVERT: C 78 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7193 (tp30) REVERT: C 243 MET cc_start: 0.8857 (mmt) cc_final: 0.8602 (mmt) outliers start: 20 outliers final: 11 residues processed: 109 average time/residue: 1.4558 time to fit residues: 165.9200 Evaluate side-chains 108 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 260 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7221 Z= 0.246 Angle : 0.599 7.974 9792 Z= 0.276 Chirality : 0.038 0.136 1101 Planarity : 0.003 0.031 1095 Dihedral : 17.145 123.734 1278 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.67 % Favored : 96.95 % Rotamer: Outliers : 2.89 % Allowed : 18.61 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.83 (0.30), residues: 786 helix: 2.88 (0.20), residues: 627 sheet: None (None), residues: 0 loop : -2.62 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 276 HIS 0.003 0.001 HIS C 266 PHE 0.017 0.002 PHE C 115 TYR 0.014 0.001 TYR C 199 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 0.763 Fit side-chains REVERT: A 14 LEU cc_start: 0.8676 (mt) cc_final: 0.8386 (mt) REVERT: A 247 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.8983 (mt) REVERT: B 172 ARG cc_start: 0.6659 (tpm170) cc_final: 0.6238 (mmp80) REVERT: B 234 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8329 (ptmm) REVERT: C 78 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7196 (tp30) REVERT: C 243 MET cc_start: 0.8875 (mmt) cc_final: 0.8574 (mmt) REVERT: C 258 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.6638 (t80) outliers start: 20 outliers final: 14 residues processed: 110 average time/residue: 1.5893 time to fit residues: 182.4830 Evaluate side-chains 115 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7221 Z= 0.241 Angle : 0.595 8.117 9792 Z= 0.276 Chirality : 0.038 0.132 1101 Planarity : 0.003 0.031 1095 Dihedral : 17.075 121.680 1278 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.29 % Favored : 97.33 % Rotamer: Outliers : 2.60 % Allowed : 18.61 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.30), residues: 786 helix: 2.88 (0.20), residues: 627 sheet: None (None), residues: 0 loop : -2.66 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 76 HIS 0.003 0.001 HIS C 266 PHE 0.016 0.002 PHE C 115 TYR 0.013 0.001 TYR C 199 ARG 0.002 0.000 ARG B 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.748 Fit side-chains REVERT: A 14 LEU cc_start: 0.8670 (mt) cc_final: 0.8374 (mt) REVERT: A 247 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.8967 (mt) REVERT: B 172 ARG cc_start: 0.6633 (tpm170) cc_final: 0.6219 (mmp80) REVERT: B 234 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8295 (ptmm) REVERT: C 78 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7193 (tp30) REVERT: C 243 MET cc_start: 0.8886 (mmt) cc_final: 0.8610 (mmt) REVERT: C 258 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.6625 (t80) outliers start: 18 outliers final: 14 residues processed: 111 average time/residue: 1.4084 time to fit residues: 163.6643 Evaluate side-chains 112 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 54 optimal weight: 0.0270 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 70 optimal weight: 0.4980 chunk 41 optimal weight: 0.0980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.133876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.097806 restraints weight = 7952.347| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.51 r_work: 0.2812 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7221 Z= 0.200 Angle : 0.574 8.218 9792 Z= 0.267 Chirality : 0.036 0.126 1101 Planarity : 0.003 0.032 1095 Dihedral : 16.654 113.220 1278 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.54 % Favored : 97.07 % Rotamer: Outliers : 2.60 % Allowed : 19.19 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.94 (0.30), residues: 786 helix: 3.00 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -2.67 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 76 HIS 0.002 0.001 HIS C 213 PHE 0.013 0.001 PHE C 115 TYR 0.011 0.001 TYR C 199 ARG 0.003 0.000 ARG B 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3204.08 seconds wall clock time: 57 minutes 31.19 seconds (3451.19 seconds total)