Starting phenix.real_space_refine on Tue Feb 13 07:36:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de9_27388/02_2024/8de9_27388_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de9_27388/02_2024/8de9_27388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de9_27388/02_2024/8de9_27388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de9_27388/02_2024/8de9_27388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de9_27388/02_2024/8de9_27388_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de9_27388/02_2024/8de9_27388_updated.pdb" } resolution = 3.4 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= 0.002 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 K 3 8.98 5 P 1 5.49 5 S 16 5.16 5 C 2760 2.51 5 N 626 2.21 5 O 709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 69": "OE1" <-> "OE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4115 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2035 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 7, 'TRANS': 251} Chain: "B" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2028 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {' K': 3, 'PEV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.84, per 1000 atoms: 0.69 Number of scatterers: 4115 At special positions: 0 Unit cell: (80.514, 97.128, 79.236, 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) K 3 19.00 S 16 16.00 P 1 15.00 O 709 8.00 N 626 7.00 C 2760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS B 93 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 761.4 milliseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 938 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 0 sheets defined 72.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 44 through 90 removed outlier: 3.569A pdb=" N ALA A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 96 through 112 Processing helix chain 'A' and resid 129 through 141 Processing helix chain 'A' and resid 153 through 195 removed outlier: 3.561A pdb=" N ILE A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 203 through 233 removed outlier: 3.894A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Proline residue: A 226 - end of helix Processing helix chain 'A' and resid 238 through 249 Processing helix chain 'A' and resid 270 through 297 Processing helix chain 'B' and resid 44 through 90 Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 96 through 112 removed outlier: 3.580A pdb=" N ALA B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 141 Processing helix chain 'B' and resid 153 through 192 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 205 through 222 Processing helix chain 'B' and resid 224 through 234 removed outlier: 4.174A pdb=" N LEU B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 249 Processing helix chain 'B' and resid 270 through 296 295 hydrogen bonds defined for protein. 885 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: 1.05 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 623 1.31 - 1.44: 1184 1.44 - 1.56: 2381 1.56 - 1.69: 3 1.69 - 1.81: 26 Bond restraints: 4217 Sorted by residual: bond pdb=" CA ILE B 264 " pdb=" C ILE B 264 " ideal model delta sigma weight residual 1.530 1.584 -0.053 1.12e-02 7.97e+03 2.27e+01 bond pdb=" C31 PEV A 401 " pdb=" O2 PEV A 401 " ideal model delta sigma weight residual 1.330 1.409 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C11 PEV A 401 " pdb=" O3 PEV A 401 " ideal model delta sigma weight residual 1.335 1.398 -0.063 2.00e-02 2.50e+03 9.77e+00 bond pdb=" CA THR A 251 " pdb=" C THR A 251 " ideal model delta sigma weight residual 1.525 1.488 0.037 1.40e-02 5.10e+03 7.01e+00 bond pdb=" N THR A 251 " pdb=" CA THR A 251 " ideal model delta sigma weight residual 1.461 1.431 0.031 1.49e-02 4.50e+03 4.26e+00 ... (remaining 4212 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.46: 60 105.46 - 112.60: 2180 112.60 - 119.74: 1429 119.74 - 126.88: 1984 126.88 - 134.03: 68 Bond angle restraints: 5721 Sorted by residual: angle pdb=" C ILE B 264 " pdb=" CA ILE B 264 " pdb=" CB ILE B 264 " ideal model delta sigma weight residual 112.19 102.19 10.00 1.15e+00 7.56e-01 7.56e+01 angle pdb=" N GLU B 263 " pdb=" CA GLU B 263 " pdb=" C GLU B 263 " ideal model delta sigma weight residual 111.17 122.10 -10.93 1.41e+00 5.03e-01 6.01e+01 angle pdb=" C GLU B 263 " pdb=" CA GLU B 263 " pdb=" CB GLU B 263 " ideal model delta sigma weight residual 112.06 101.34 10.72 1.57e+00 4.06e-01 4.66e+01 angle pdb=" N TRP A 199 " pdb=" CA TRP A 199 " pdb=" C TRP A 199 " ideal model delta sigma weight residual 108.52 118.91 -10.39 1.63e+00 3.76e-01 4.06e+01 angle pdb=" O3P PEV A 401 " pdb=" P PEV A 401 " pdb=" O4P PEV A 401 " ideal model delta sigma weight residual 93.57 109.93 -16.36 3.00e+00 1.11e-01 2.98e+01 ... (remaining 5716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.26: 2302 27.26 - 54.53: 105 54.53 - 81.79: 8 81.79 - 109.05: 0 109.05 - 136.32: 1 Dihedral angle restraints: 2416 sinusoidal: 947 harmonic: 1469 Sorted by residual: dihedral pdb=" CA GLN B 122 " pdb=" C GLN B 122 " pdb=" N GLU B 123 " pdb=" CA GLU B 123 " ideal model delta harmonic sigma weight residual 180.00 150.90 29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" C3 PEV A 401 " pdb=" C1 PEV A 401 " pdb=" C2 PEV A 401 " pdb=" O3P PEV A 401 " ideal model delta sinusoidal sigma weight residual 292.80 156.48 136.32 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" CA LEU B 68 " pdb=" C LEU B 68 " pdb=" N GLU B 69 " pdb=" CA GLU B 69 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 2413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 591 0.089 - 0.178: 68 0.178 - 0.266: 5 0.266 - 0.355: 1 0.355 - 0.444: 2 Chirality restraints: 667 Sorted by residual: chirality pdb=" CA THR A 251 " pdb=" N THR A 251 " pdb=" C THR A 251 " pdb=" CB THR A 251 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" CA ILE B 264 " pdb=" N ILE B 264 " pdb=" C ILE B 264 " pdb=" CB ILE B 264 " both_signs ideal model delta sigma weight residual False 2.43 2.79 -0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA LEU A 249 " pdb=" N LEU A 249 " pdb=" C LEU A 249 " pdb=" CB LEU A 249 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 664 not shown) Planarity restraints: 685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 119 " 0.057 5.00e-02 4.00e+02 8.76e-02 1.23e+01 pdb=" N PRO A 120 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 120 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 120 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 115 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO A 116 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 116 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 116 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 196 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.45e+00 pdb=" C PHE A 196 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE A 196 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL A 197 " -0.013 2.00e-02 2.50e+03 ... (remaining 682 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.88: 1456 2.88 - 3.44: 5059 3.44 - 4.01: 7323 4.01 - 4.57: 10295 4.57 - 5.14: 14449 Nonbonded interactions: 38582 Sorted by model distance: nonbonded pdb=" OE2 GLU A 234 " pdb=" OH TYR A 266 " model vdw 2.309 2.440 nonbonded pdb=" O PRO A 116 " pdb=" NZ LYS B 84 " model vdw 2.335 2.520 nonbonded pdb=" NZ LYS A 84 " pdb=" O PRO B 116 " model vdw 2.349 2.520 nonbonded pdb=" C ILE A 264 " pdb=" OE1 GLU A 265 " model vdw 2.376 3.270 nonbonded pdb=" OE1 GLN A 231 " pdb=" OG SER A 241 " model vdw 2.414 2.440 ... (remaining 38577 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' and resid 40 through 297) selection = chain 'B' } 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: 0.320 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: 1.710 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.190 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 : 0.005 0.079 4217 Z= 0.309 Angle : 1.125 16.364 5721 Z= 0.634 Chirality : 0.059 0.444 667 Planarity : 0.008 0.088 685 Dihedral : 14.378 136.317 1475 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.23 % Allowed : 2.06 % Favored : 97.71 % 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: 2.27 (0.35), residues: 513 helix: 2.42 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -1.75 (0.51), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 127 HIS 0.006 0.001 HIS B 91 PHE 0.039 0.003 PHE A 276 TYR 0.016 0.002 TYR B 284 ARG 0.003 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8274 (tttt) cc_final: 0.7237 (ttmm) REVERT: A 77 LYS cc_start: 0.9185 (mttm) cc_final: 0.8964 (mtpt) REVERT: A 82 GLN cc_start: 0.8363 (pt0) cc_final: 0.7630 (pp30) REVERT: A 86 ASP cc_start: 0.8291 (m-30) cc_final: 0.7641 (m-30) REVERT: A 104 LYS cc_start: 0.9424 (ttpp) cc_final: 0.9104 (ttpp) REVERT: A 105 GLN cc_start: 0.8742 (mt0) cc_final: 0.8438 (pt0) REVERT: A 195 MET cc_start: 0.8544 (tmm) cc_final: 0.7513 (tmm) REVERT: A 268 ASP cc_start: 0.7318 (t70) cc_final: 0.6974 (t0) REVERT: B 66 LYS cc_start: 0.8656 (ttpt) cc_final: 0.8149 (ttmm) REVERT: B 120 PRO cc_start: 0.8391 (Cg_endo) cc_final: 0.7369 (Cg_exo) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.1644 time to fit residues: 45.6719 Evaluate side-chains 193 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 23 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4217 Z= 0.221 Angle : 0.752 7.003 5721 Z= 0.386 Chirality : 0.044 0.209 667 Planarity : 0.005 0.042 685 Dihedral : 10.406 139.795 586 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.66 % Allowed : 16.70 % Favored : 79.63 % 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: 2.67 (0.36), residues: 513 helix: 2.66 (0.24), residues: 396 sheet: None (None), residues: 0 loop : -1.58 (0.53), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 199 HIS 0.008 0.002 HIS B 91 PHE 0.020 0.002 PHE A 158 TYR 0.015 0.002 TYR B 57 ARG 0.002 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8324 (tttt) cc_final: 0.7445 (ttmm) REVERT: A 73 GLU cc_start: 0.8478 (pt0) cc_final: 0.8217 (pt0) REVERT: A 79 ARG cc_start: 0.8357 (tmt-80) cc_final: 0.8099 (tmt-80) REVERT: A 82 GLN cc_start: 0.8426 (pt0) cc_final: 0.7841 (pp30) REVERT: A 86 ASP cc_start: 0.8172 (m-30) cc_final: 0.7836 (m-30) REVERT: A 101 ASP cc_start: 0.8385 (t0) cc_final: 0.8169 (t0) REVERT: A 104 LYS cc_start: 0.9415 (ttpp) cc_final: 0.9017 (ttpp) REVERT: A 153 GLU cc_start: 0.7743 (pm20) cc_final: 0.7477 (pm20) REVERT: A 263 GLU cc_start: 0.7561 (tt0) cc_final: 0.7279 (tt0) REVERT: B 66 LYS cc_start: 0.8860 (ttpt) cc_final: 0.8076 (ttmm) REVERT: B 122 GLN cc_start: 0.6952 (mp-120) cc_final: 0.6197 (mp10) REVERT: B 222 PHE cc_start: 0.7539 (m-80) cc_final: 0.7283 (m-10) REVERT: B 240 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7680 (mt-10) outliers start: 16 outliers final: 6 residues processed: 210 average time/residue: 0.1670 time to fit residues: 42.8763 Evaluate side-chains 197 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 191 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.0170 chunk 45 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 180 GLN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4217 Z= 0.233 Angle : 0.765 11.470 5721 Z= 0.382 Chirality : 0.044 0.195 667 Planarity : 0.005 0.051 685 Dihedral : 10.364 136.387 586 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.81 % Allowed : 20.14 % Favored : 75.06 % 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: 2.54 (0.36), residues: 513 helix: 2.56 (0.24), residues: 394 sheet: None (None), residues: 0 loop : -1.50 (0.54), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 295 HIS 0.002 0.001 HIS B 151 PHE 0.021 0.002 PHE A 217 TYR 0.021 0.002 TYR A 57 ARG 0.003 0.001 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 202 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8066 (tttt) cc_final: 0.7310 (ttmm) REVERT: A 73 GLU cc_start: 0.8613 (pt0) cc_final: 0.8343 (pt0) REVERT: A 82 GLN cc_start: 0.8394 (pt0) cc_final: 0.7663 (pp30) REVERT: A 83 GLU cc_start: 0.8194 (tp30) cc_final: 0.7804 (tp30) REVERT: A 86 ASP cc_start: 0.8297 (m-30) cc_final: 0.7663 (m-30) REVERT: A 101 ASP cc_start: 0.8417 (t0) cc_final: 0.8154 (t0) REVERT: A 104 LYS cc_start: 0.9421 (ttpp) cc_final: 0.9095 (ttpp) REVERT: A 268 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6762 (t70) REVERT: B 66 LYS cc_start: 0.8876 (ttpt) cc_final: 0.8144 (ttmm) REVERT: B 105 GLN cc_start: 0.7549 (mt0) cc_final: 0.7277 (mt0) REVERT: B 295 TRP cc_start: 0.7512 (OUTLIER) cc_final: 0.6888 (m100) outliers start: 21 outliers final: 12 residues processed: 205 average time/residue: 0.1688 time to fit residues: 42.0104 Evaluate side-chains 209 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 195 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 295 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 13 optimal weight: 0.0670 chunk 40 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4217 Z= 0.230 Angle : 0.767 10.889 5721 Z= 0.382 Chirality : 0.043 0.178 667 Planarity : 0.004 0.038 685 Dihedral : 10.365 133.693 586 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.12 % Allowed : 24.49 % Favored : 71.40 % 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: 2.44 (0.36), residues: 513 helix: 2.46 (0.25), residues: 396 sheet: None (None), residues: 0 loop : -1.50 (0.54), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 295 HIS 0.008 0.001 HIS B 91 PHE 0.019 0.002 PHE A 217 TYR 0.018 0.002 TYR B 57 ARG 0.004 0.001 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 201 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8143 (tttt) cc_final: 0.7512 (ttmm) REVERT: A 73 GLU cc_start: 0.8638 (pt0) cc_final: 0.8416 (pt0) REVERT: A 82 GLN cc_start: 0.8437 (pt0) cc_final: 0.7754 (pp30) REVERT: A 86 ASP cc_start: 0.8266 (m-30) cc_final: 0.7677 (m-30) REVERT: A 94 VAL cc_start: 0.8935 (t) cc_final: 0.8721 (m) REVERT: A 101 ASP cc_start: 0.8419 (t0) cc_final: 0.8178 (t0) REVERT: A 104 LYS cc_start: 0.9400 (ttpp) cc_final: 0.9097 (ttpp) REVERT: A 207 ARG cc_start: 0.8386 (ttp-110) cc_final: 0.7934 (ttp-110) REVERT: B 43 LYS cc_start: 0.7511 (tptt) cc_final: 0.7186 (tptt) REVERT: B 58 LEU cc_start: 0.8859 (mt) cc_final: 0.8518 (mp) REVERT: B 66 LYS cc_start: 0.8940 (ttpt) cc_final: 0.8197 (ttmm) REVERT: B 86 ASP cc_start: 0.8499 (p0) cc_final: 0.8023 (p0) REVERT: B 100 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8543 (mm-30) REVERT: B 104 LYS cc_start: 0.9276 (ttmm) cc_final: 0.8929 (mtmm) REVERT: B 194 LYS cc_start: 0.7726 (pttt) cc_final: 0.7127 (pttm) REVERT: B 195 MET cc_start: 0.7618 (mmm) cc_final: 0.7272 (mpp) REVERT: B 291 MET cc_start: 0.8220 (tmm) cc_final: 0.7843 (mmp) outliers start: 18 outliers final: 11 residues processed: 207 average time/residue: 0.1729 time to fit residues: 43.6015 Evaluate side-chains 202 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 191 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 4217 Z= 0.252 Angle : 0.808 11.198 5721 Z= 0.402 Chirality : 0.044 0.174 667 Planarity : 0.004 0.039 685 Dihedral : 10.334 131.593 586 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.20 % Allowed : 27.00 % Favored : 69.79 % 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: 2.24 (0.36), residues: 513 helix: 2.32 (0.25), residues: 395 sheet: None (None), residues: 0 loop : -1.55 (0.55), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 295 HIS 0.003 0.001 HIS A 91 PHE 0.020 0.002 PHE A 158 TYR 0.019 0.002 TYR B 57 ARG 0.004 0.001 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 201 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.7853 (mmtt) cc_final: 0.7602 (mmtm) REVERT: A 66 LYS cc_start: 0.8190 (tttt) cc_final: 0.7432 (ttmm) REVERT: A 73 GLU cc_start: 0.8561 (pt0) cc_final: 0.8347 (pt0) REVERT: A 82 GLN cc_start: 0.8480 (pt0) cc_final: 0.7717 (pp30) REVERT: A 83 GLU cc_start: 0.8125 (tp30) cc_final: 0.7624 (tp30) REVERT: A 86 ASP cc_start: 0.8260 (m-30) cc_final: 0.7843 (m-30) REVERT: B 58 LEU cc_start: 0.8872 (mt) cc_final: 0.8534 (mt) REVERT: B 66 LYS cc_start: 0.8929 (ttpt) cc_final: 0.8688 (ttpp) REVERT: B 86 ASP cc_start: 0.8551 (p0) cc_final: 0.8225 (p0) REVERT: B 104 LYS cc_start: 0.9257 (ttmm) cc_final: 0.8908 (mtmm) outliers start: 14 outliers final: 9 residues processed: 207 average time/residue: 0.1663 time to fit residues: 41.8891 Evaluate side-chains 194 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 185 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 25 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4217 Z= 0.230 Angle : 0.821 11.904 5721 Z= 0.400 Chirality : 0.043 0.162 667 Planarity : 0.004 0.045 685 Dihedral : 10.261 129.564 586 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.35 % Allowed : 26.77 % Favored : 68.88 % 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 (0.37), residues: 513 helix: 2.42 (0.25), residues: 393 sheet: None (None), residues: 0 loop : -1.67 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 295 HIS 0.001 0.001 HIS B 91 PHE 0.021 0.001 PHE A 158 TYR 0.013 0.002 TYR A 162 ARG 0.010 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 194 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.7787 (mmtt) cc_final: 0.7578 (mmtm) REVERT: A 66 LYS cc_start: 0.8181 (tttt) cc_final: 0.7440 (ttmm) REVERT: A 82 GLN cc_start: 0.8463 (pt0) cc_final: 0.7652 (pp30) REVERT: A 83 GLU cc_start: 0.8029 (tp30) cc_final: 0.7370 (tp30) REVERT: A 86 ASP cc_start: 0.8257 (m-30) cc_final: 0.7882 (m-30) REVERT: B 51 PHE cc_start: 0.9204 (t80) cc_final: 0.8965 (t80) REVERT: B 58 LEU cc_start: 0.8863 (mt) cc_final: 0.8529 (mt) REVERT: B 66 LYS cc_start: 0.8926 (ttpt) cc_final: 0.8567 (ttmm) REVERT: B 86 ASP cc_start: 0.8591 (p0) cc_final: 0.8252 (p0) outliers start: 19 outliers final: 10 residues processed: 203 average time/residue: 0.1480 time to fit residues: 36.6697 Evaluate side-chains 196 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 186 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 221 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN B 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4217 Z= 0.248 Angle : 0.841 11.961 5721 Z= 0.411 Chirality : 0.044 0.161 667 Planarity : 0.004 0.038 685 Dihedral : 10.139 128.306 586 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.97 % Allowed : 30.89 % Favored : 66.13 % 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: 2.23 (0.37), residues: 513 helix: 2.40 (0.25), residues: 392 sheet: None (None), residues: 0 loop : -1.80 (0.54), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 199 HIS 0.001 0.000 HIS B 151 PHE 0.025 0.002 PHE A 158 TYR 0.020 0.002 TYR B 57 ARG 0.008 0.001 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 189 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.7811 (mmtt) cc_final: 0.7592 (mmtm) REVERT: A 66 LYS cc_start: 0.8206 (tttt) cc_final: 0.7481 (ttmm) REVERT: A 82 GLN cc_start: 0.8538 (pt0) cc_final: 0.7670 (pp30) REVERT: A 83 GLU cc_start: 0.8191 (tp30) cc_final: 0.7810 (tp30) REVERT: A 86 ASP cc_start: 0.8201 (m-30) cc_final: 0.7794 (m-30) REVERT: A 99 LEU cc_start: 0.9286 (mt) cc_final: 0.9030 (pp) REVERT: A 174 LEU cc_start: 0.8735 (tp) cc_final: 0.8292 (tp) REVERT: B 51 PHE cc_start: 0.9208 (t80) cc_final: 0.8947 (t80) REVERT: B 58 LEU cc_start: 0.8903 (mt) cc_final: 0.8560 (mt) REVERT: B 66 LYS cc_start: 0.8939 (ttpt) cc_final: 0.8299 (ttmm) REVERT: B 86 ASP cc_start: 0.8596 (p0) cc_final: 0.8263 (p0) outliers start: 13 outliers final: 8 residues processed: 194 average time/residue: 0.1644 time to fit residues: 39.0092 Evaluate side-chains 182 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 174 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 221 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 0.0970 chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4217 Z= 0.235 Angle : 0.905 16.844 5721 Z= 0.425 Chirality : 0.044 0.174 667 Planarity : 0.004 0.044 685 Dihedral : 9.999 126.265 586 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.52 % Allowed : 31.35 % Favored : 66.13 % 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: 2.12 (0.37), residues: 513 helix: 2.29 (0.25), residues: 392 sheet: None (None), residues: 0 loop : -1.71 (0.55), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 199 HIS 0.002 0.000 HIS B 91 PHE 0.024 0.001 PHE A 158 TYR 0.014 0.002 TYR A 284 ARG 0.006 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 196 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8212 (tttt) cc_final: 0.7462 (ttmm) REVERT: A 82 GLN cc_start: 0.8509 (pt0) cc_final: 0.7728 (pp30) REVERT: A 83 GLU cc_start: 0.8244 (tp30) cc_final: 0.7568 (tp30) REVERT: A 86 ASP cc_start: 0.8209 (m-30) cc_final: 0.7638 (m-30) REVERT: A 101 ASP cc_start: 0.8377 (t0) cc_final: 0.7355 (t0) REVERT: A 198 LYS cc_start: 0.8390 (pptt) cc_final: 0.8040 (mtmm) REVERT: B 58 LEU cc_start: 0.8911 (mt) cc_final: 0.8534 (mt) REVERT: B 66 LYS cc_start: 0.8945 (ttpt) cc_final: 0.8314 (ttmm) REVERT: B 86 ASP cc_start: 0.8562 (p0) cc_final: 0.8242 (p0) REVERT: B 291 MET cc_start: 0.7808 (tmm) cc_final: 0.7447 (mmp) outliers start: 11 outliers final: 8 residues processed: 200 average time/residue: 0.1579 time to fit residues: 38.8968 Evaluate side-chains 186 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 178 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.0670 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4217 Z= 0.253 Angle : 0.952 12.593 5721 Z= 0.461 Chirality : 0.046 0.192 667 Planarity : 0.004 0.041 685 Dihedral : 9.881 124.062 586 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.06 % Allowed : 33.64 % Favored : 64.30 % 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: 1.90 (0.37), residues: 513 helix: 2.09 (0.25), residues: 394 sheet: None (None), residues: 0 loop : -1.68 (0.55), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 199 HIS 0.002 0.001 HIS B 91 PHE 0.023 0.001 PHE B 158 TYR 0.022 0.002 TYR A 162 ARG 0.010 0.001 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 187 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8226 (tttt) cc_final: 0.7442 (ttmm) REVERT: A 75 LEU cc_start: 0.9216 (pt) cc_final: 0.8935 (pt) REVERT: A 82 GLN cc_start: 0.8559 (pt0) cc_final: 0.7815 (pp30) REVERT: A 86 ASP cc_start: 0.8211 (m-30) cc_final: 0.7597 (m-30) REVERT: A 99 LEU cc_start: 0.9261 (mt) cc_final: 0.9008 (pp) REVERT: A 198 LYS cc_start: 0.8378 (pptt) cc_final: 0.8045 (mtmm) REVERT: B 58 LEU cc_start: 0.8932 (mt) cc_final: 0.8588 (mt) REVERT: B 66 LYS cc_start: 0.8935 (ttpt) cc_final: 0.8679 (ttpp) REVERT: B 86 ASP cc_start: 0.8538 (p0) cc_final: 0.7824 (p0) REVERT: B 291 MET cc_start: 0.8104 (tmm) cc_final: 0.7613 (mmp) outliers start: 9 outliers final: 8 residues processed: 190 average time/residue: 0.1626 time to fit residues: 37.9024 Evaluate side-chains 189 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 181 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4217 Z= 0.290 Angle : 0.958 12.118 5721 Z= 0.470 Chirality : 0.047 0.185 667 Planarity : 0.004 0.042 685 Dihedral : 9.854 122.883 586 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.52 % Allowed : 34.55 % Favored : 62.93 % 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: 1.81 (0.36), residues: 513 helix: 2.05 (0.25), residues: 393 sheet: None (None), residues: 0 loop : -1.77 (0.53), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 295 HIS 0.002 0.001 HIS B 91 PHE 0.026 0.002 PHE B 158 TYR 0.020 0.002 TYR A 162 ARG 0.010 0.001 ARG A 207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 169 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8264 (tttt) cc_final: 0.7484 (ttmm) REVERT: A 68 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8216 (mp) REVERT: A 82 GLN cc_start: 0.8529 (pt0) cc_final: 0.7781 (pp30) REVERT: A 83 GLU cc_start: 0.8206 (tp30) cc_final: 0.7864 (tp30) REVERT: A 86 ASP cc_start: 0.8279 (m-30) cc_final: 0.7680 (m-30) REVERT: A 198 LYS cc_start: 0.8382 (pptt) cc_final: 0.8045 (mtmm) REVERT: B 66 LYS cc_start: 0.8978 (ttpt) cc_final: 0.8679 (ttpp) REVERT: B 86 ASP cc_start: 0.8562 (p0) cc_final: 0.7830 (p0) REVERT: B 282 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8244 (mt) REVERT: B 291 MET cc_start: 0.7955 (tmm) cc_final: 0.7523 (mmp) outliers start: 11 outliers final: 8 residues processed: 173 average time/residue: 0.1700 time to fit residues: 35.9373 Evaluate side-chains 175 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 165 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.153197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.117342 restraints weight = 7329.722| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.79 r_work: 0.3408 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4217 Z= 0.269 Angle : 0.966 11.715 5721 Z= 0.477 Chirality : 0.047 0.187 667 Planarity : 0.004 0.040 685 Dihedral : 9.865 122.082 586 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.90 % Favored : 95.91 % Rotamer: Outliers : 2.75 % Allowed : 35.70 % Favored : 61.56 % 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: 1.88 (0.36), residues: 513 helix: 2.11 (0.25), residues: 392 sheet: None (None), residues: 0 loop : -1.78 (0.52), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 295 HIS 0.002 0.001 HIS A 232 PHE 0.027 0.001 PHE B 158 TYR 0.025 0.002 TYR B 57 ARG 0.015 0.001 ARG A 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1464.37 seconds wall clock time: 27 minutes 12.61 seconds (1632.61 seconds total)