Starting phenix.real_space_refine on Wed Mar 5 22:13:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g2w_50986/03_2025/9g2w_50986.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g2w_50986/03_2025/9g2w_50986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g2w_50986/03_2025/9g2w_50986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g2w_50986/03_2025/9g2w_50986.map" model { file = "/net/cci-nas-00/data/ceres_data/9g2w_50986/03_2025/9g2w_50986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g2w_50986/03_2025/9g2w_50986.cif" } resolution = 3.6 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2404 2.51 5 N 677 2.21 5 O 741 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3838 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1939 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain: "B" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1899 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 1 Time building chain proxies: 2.93, per 1000 atoms: 0.76 Number of scatterers: 3838 At special positions: 0 Unit cell: (114.208, 83.664, 115.536, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 741 8.00 N 677 7.00 C 2404 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 - 3.00 Amino acid : True - 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: 1.08 Conformation dependent library (CDL) restraints added in 435.8 milliseconds 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 914 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 93.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 11 through 30 removed outlier: 3.654A pdb=" N ALA A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 68 Processing helix chain 'A' and resid 70 through 84 removed outlier: 3.578A pdb=" N ARG A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 109 Processing helix chain 'A' and resid 112 through 143 Processing helix chain 'A' and resid 143 through 181 removed outlier: 4.107A pdb=" N TYR A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 215 removed outlier: 3.972A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 252 removed outlier: 3.884A pdb=" N THR A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 30 Processing helix chain 'B' and resid 39 through 68 Processing helix chain 'B' and resid 70 through 84 removed outlier: 3.520A pdb=" N ARG B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 109 Processing helix chain 'B' and resid 112 through 143 Processing helix chain 'B' and resid 143 through 153 removed outlier: 3.529A pdb=" N LEU B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 181 removed outlier: 3.541A pdb=" N THR B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 215 Processing helix chain 'B' and resid 215 through 252 367 hydrogen bonds defined for protein. 1101 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: 1.00 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 859 1.33 - 1.45: 760 1.45 - 1.57: 2248 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3891 Sorted by residual: bond pdb=" N ILE A 91 " pdb=" CA ILE A 91 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.20e-02 6.94e+03 8.44e+00 bond pdb=" N ILE A 216 " pdb=" CA ILE A 216 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.26e-02 6.30e+03 7.96e+00 bond pdb=" N ASN A 93 " pdb=" CA ASN A 93 " ideal model delta sigma weight residual 1.462 1.488 -0.026 9.50e-03 1.11e+04 7.61e+00 bond pdb=" N ILE A 75 " pdb=" CA ILE A 75 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.59e+00 bond pdb=" N ILE B 151 " pdb=" CA ILE B 151 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.26e-02 6.30e+03 7.58e+00 ... (remaining 3886 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 3763 1.04 - 2.09: 775 2.09 - 3.13: 652 3.13 - 4.18: 36 4.18 - 5.22: 9 Bond angle restraints: 5235 Sorted by residual: angle pdb=" N LEU A 30 " pdb=" CA LEU A 30 " pdb=" C LEU A 30 " ideal model delta sigma weight residual 112.87 108.08 4.79 1.20e+00 6.94e-01 1.59e+01 angle pdb=" N GLY A 31 " pdb=" CA GLY A 31 " pdb=" C GLY A 31 " ideal model delta sigma weight residual 115.40 110.27 5.13 1.32e+00 5.74e-01 1.51e+01 angle pdb=" N GLU B 214 " pdb=" CA GLU B 214 " pdb=" C GLU B 214 " ideal model delta sigma weight residual 113.23 108.50 4.73 1.24e+00 6.50e-01 1.45e+01 angle pdb=" CA ALA B 182 " pdb=" C ALA B 182 " pdb=" O ALA B 182 " ideal model delta sigma weight residual 122.64 118.13 4.51 1.25e+00 6.40e-01 1.30e+01 angle pdb=" N LEU A 83 " pdb=" CA LEU A 83 " pdb=" C LEU A 83 " ideal model delta sigma weight residual 113.01 108.81 4.20 1.20e+00 6.94e-01 1.23e+01 ... (remaining 5230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.50: 2167 15.50 - 31.00: 169 31.00 - 46.50: 47 46.50 - 62.00: 30 62.00 - 77.50: 6 Dihedral angle restraints: 2419 sinusoidal: 1014 harmonic: 1405 Sorted by residual: dihedral pdb=" CD ARG B 210 " pdb=" NE ARG B 210 " pdb=" CZ ARG B 210 " pdb=" NH1 ARG B 210 " ideal model delta sinusoidal sigma weight residual 0.00 32.61 -32.61 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" CD ARG B 169 " pdb=" NE ARG B 169 " pdb=" CZ ARG B 169 " pdb=" NH1 ARG B 169 " ideal model delta sinusoidal sigma weight residual 0.00 -27.47 27.47 1 1.00e+01 1.00e-02 1.08e+01 dihedral pdb=" CD ARG B 225 " pdb=" NE ARG B 225 " pdb=" CZ ARG B 225 " pdb=" NH1 ARG B 225 " ideal model delta sinusoidal sigma weight residual 0.00 -26.98 26.98 1 1.00e+01 1.00e-02 1.05e+01 ... (remaining 2416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 271 0.043 - 0.085: 105 0.085 - 0.127: 124 0.127 - 0.169: 62 0.169 - 0.211: 28 Chirality restraints: 590 Sorted by residual: chirality pdb=" CA ILE A 208 " pdb=" N ILE A 208 " pdb=" C ILE A 208 " pdb=" CB ILE A 208 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ASP B 203 " pdb=" N ASP B 203 " pdb=" C ASP B 203 " pdb=" CB ASP B 203 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE A 75 " pdb=" N ILE A 75 " pdb=" C ILE A 75 " pdb=" CB ILE A 75 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 587 not shown) Planarity restraints: 681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 210 " -0.574 9.50e-02 1.11e+02 2.57e-01 4.04e+01 pdb=" NE ARG B 210 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG B 210 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 210 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 210 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 169 " -0.493 9.50e-02 1.11e+02 2.21e-01 2.99e+01 pdb=" NE ARG B 169 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG B 169 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 169 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 169 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 225 " 0.487 9.50e-02 1.11e+02 2.18e-01 2.92e+01 pdb=" NE ARG B 225 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 225 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 225 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 225 " 0.016 2.00e-02 2.50e+03 ... (remaining 678 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1456 2.86 - 3.37: 4479 3.37 - 3.88: 6652 3.88 - 4.39: 7661 4.39 - 4.90: 11287 Nonbonded interactions: 31535 Sorted by model distance: nonbonded pdb=" O SER B 200 " pdb=" OD1 ASP B 203 " model vdw 2.354 3.040 nonbonded pdb=" O LEU B 195 " pdb=" OG1 THR B 198 " model vdw 2.399 3.040 nonbonded pdb=" NE2 GLN A 243 " pdb=" OD1 ASP A 247 " model vdw 2.399 3.120 nonbonded pdb=" O ASP A 14 " pdb=" OG1 THR A 17 " model vdw 2.414 3.040 nonbonded pdb=" N GLU A 186 " pdb=" OE1 GLU A 186 " model vdw 2.419 3.120 ... (remaining 31530 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 30 or resid 35 through 252)) 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.560 Find NCS groups from input model: 0.130 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 : 0.009 0.044 3891 Z= 0.567 Angle : 1.167 5.221 5235 Z= 0.968 Chirality : 0.084 0.211 590 Planarity : 0.024 0.257 681 Dihedral : 14.466 77.496 1505 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.73 % Allowed : 5.11 % Favored : 94.16 % 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: -0.44 (0.34), residues: 472 helix: -0.00 (0.22), residues: 430 sheet: None (None), residues: 0 loop : -1.86 (0.79), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 55 HIS 0.007 0.002 HIS B 41 PHE 0.028 0.002 PHE B 78 TYR 0.023 0.002 TYR A 244 ARG 0.036 0.004 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8484 (tm-30) REVERT: B 235 MET cc_start: 0.8855 (tmm) cc_final: 0.8616 (tmm) outliers start: 3 outliers final: 0 residues processed: 78 average time/residue: 0.1560 time to fit residues: 15.1550 Evaluate side-chains 43 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN B 228 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.061532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.048071 restraints weight = 18710.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.049695 restraints weight = 8436.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.050718 restraints weight = 5050.459| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3891 Z= 0.179 Angle : 0.534 9.727 5235 Z= 0.289 Chirality : 0.033 0.122 590 Planarity : 0.004 0.032 681 Dihedral : 3.015 12.251 521 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.46 % Allowed : 9.49 % Favored : 89.05 % 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: 4.80 (0.35), residues: 472 helix: 3.38 (0.22), residues: 435 sheet: None (None), residues: 0 loop : -0.24 (0.89), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 55 HIS 0.007 0.001 HIS A 41 PHE 0.021 0.002 PHE B 78 TYR 0.019 0.001 TYR A 244 ARG 0.006 0.001 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7436 (mt-10) REVERT: A 121 CYS cc_start: 0.8342 (t) cc_final: 0.8018 (t) REVERT: B 64 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8491 (tm-30) REVERT: B 125 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8584 (mp10) REVERT: B 235 MET cc_start: 0.8994 (tmm) cc_final: 0.8640 (tmm) REVERT: B 245 MET cc_start: 0.9276 (tpp) cc_final: 0.8974 (tpp) outliers start: 6 outliers final: 3 residues processed: 55 average time/residue: 0.1786 time to fit residues: 12.3906 Evaluate side-chains 44 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 234 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 20 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.061110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.047930 restraints weight = 18725.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.049527 restraints weight = 8436.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.050538 restraints weight = 5060.328| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3891 Z= 0.171 Angle : 0.549 9.640 5235 Z= 0.280 Chirality : 0.033 0.118 590 Planarity : 0.004 0.034 681 Dihedral : 2.986 12.506 521 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.19 % Allowed : 9.73 % Favored : 88.08 % 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: 5.99 (0.35), residues: 472 helix: 4.15 (0.22), residues: 434 sheet: None (None), residues: 0 loop : 0.28 (0.93), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 55 HIS 0.009 0.002 HIS A 41 PHE 0.024 0.002 PHE A 25 TYR 0.020 0.001 TYR A 244 ARG 0.003 0.001 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 CYS cc_start: 0.8327 (t) cc_final: 0.7933 (t) REVERT: A 179 LEU cc_start: 0.9375 (tt) cc_final: 0.9090 (pp) REVERT: B 103 ASP cc_start: 0.8684 (t0) cc_final: 0.8190 (t0) REVERT: B 125 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8565 (mp10) REVERT: B 235 MET cc_start: 0.8976 (tmm) cc_final: 0.8708 (tmm) REVERT: B 245 MET cc_start: 0.9288 (tpp) cc_final: 0.8969 (tpp) outliers start: 9 outliers final: 4 residues processed: 49 average time/residue: 0.1393 time to fit residues: 8.9662 Evaluate side-chains 42 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.061119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.047946 restraints weight = 19128.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.049501 restraints weight = 8697.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.050490 restraints weight = 5272.088| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3891 Z= 0.166 Angle : 0.508 7.456 5235 Z= 0.268 Chirality : 0.032 0.115 590 Planarity : 0.003 0.032 681 Dihedral : 3.010 12.215 521 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.22 % Allowed : 11.68 % Favored : 87.10 % 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: 6.11 (0.35), residues: 472 helix: 4.22 (0.22), residues: 435 sheet: None (None), residues: 0 loop : 0.22 (0.93), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 55 HIS 0.008 0.001 HIS A 41 PHE 0.010 0.001 PHE B 78 TYR 0.012 0.001 TYR B 242 ARG 0.003 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 CYS cc_start: 0.8496 (t) cc_final: 0.8070 (t) REVERT: B 125 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8590 (mp10) REVERT: B 245 MET cc_start: 0.9208 (tpp) cc_final: 0.8898 (tpp) outliers start: 5 outliers final: 3 residues processed: 41 average time/residue: 0.1444 time to fit residues: 7.8070 Evaluate side-chains 37 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 165 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.061043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.047878 restraints weight = 19900.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.049402 restraints weight = 9004.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.050408 restraints weight = 5446.003| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3891 Z= 0.165 Angle : 0.511 6.799 5235 Z= 0.265 Chirality : 0.032 0.128 590 Planarity : 0.003 0.030 681 Dihedral : 3.098 16.211 521 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.43 % Allowed : 10.71 % Favored : 86.86 % 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: 6.18 (0.35), residues: 472 helix: 4.27 (0.22), residues: 435 sheet: None (None), residues: 0 loop : 0.28 (0.93), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 55 HIS 0.008 0.001 HIS A 41 PHE 0.015 0.001 PHE B 78 TYR 0.024 0.001 TYR B 242 ARG 0.004 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 CYS cc_start: 0.8514 (t) cc_final: 0.8072 (t) REVERT: A 235 MET cc_start: 0.9015 (tpp) cc_final: 0.8541 (tmm) REVERT: B 103 ASP cc_start: 0.8710 (t0) cc_final: 0.8113 (t0) REVERT: B 125 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8585 (mp10) REVERT: B 245 MET cc_start: 0.9225 (tpp) cc_final: 0.8828 (tpp) outliers start: 10 outliers final: 6 residues processed: 44 average time/residue: 0.1391 time to fit residues: 8.0876 Evaluate side-chains 44 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.061130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.047727 restraints weight = 19526.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.049269 restraints weight = 9017.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.050243 restraints weight = 5516.278| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3891 Z= 0.167 Angle : 0.527 8.134 5235 Z= 0.269 Chirality : 0.032 0.155 590 Planarity : 0.003 0.029 681 Dihedral : 3.110 16.255 521 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.19 % Allowed : 11.68 % Favored : 86.13 % 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: 6.19 (0.35), residues: 472 helix: 4.27 (0.22), residues: 435 sheet: None (None), residues: 0 loop : 0.34 (0.94), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 55 HIS 0.008 0.001 HIS A 41 PHE 0.026 0.002 PHE A 78 TYR 0.021 0.001 TYR B 242 ARG 0.002 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 CYS cc_start: 0.8507 (t) cc_final: 0.8072 (t) REVERT: A 235 MET cc_start: 0.9001 (tpp) cc_final: 0.8478 (tmm) REVERT: B 125 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8601 (mp10) REVERT: B 248 LEU cc_start: 0.8557 (tt) cc_final: 0.8334 (tt) outliers start: 9 outliers final: 7 residues processed: 46 average time/residue: 0.1582 time to fit residues: 9.5319 Evaluate side-chains 46 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.061554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.048208 restraints weight = 19269.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.049730 restraints weight = 8900.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.050722 restraints weight = 5472.673| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3891 Z= 0.155 Angle : 0.532 7.898 5235 Z= 0.269 Chirality : 0.032 0.177 590 Planarity : 0.003 0.029 681 Dihedral : 3.103 16.924 521 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.43 % Allowed : 11.92 % Favored : 85.64 % 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: 6.22 (0.35), residues: 472 helix: 4.29 (0.22), residues: 435 sheet: None (None), residues: 0 loop : 0.28 (0.94), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 55 HIS 0.014 0.002 HIS A 41 PHE 0.026 0.002 PHE A 78 TYR 0.018 0.002 TYR B 242 ARG 0.005 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.9004 (tpp) cc_final: 0.8470 (tmm) REVERT: B 103 ASP cc_start: 0.8727 (t0) cc_final: 0.8048 (t0) REVERT: B 125 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8605 (mp10) REVERT: B 245 MET cc_start: 0.9143 (tpp) cc_final: 0.8912 (tpp) outliers start: 10 outliers final: 6 residues processed: 48 average time/residue: 0.1493 time to fit residues: 9.3058 Evaluate side-chains 43 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.060858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.047258 restraints weight = 19460.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.048840 restraints weight = 9013.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.049833 restraints weight = 5572.836| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3891 Z= 0.167 Angle : 0.571 10.800 5235 Z= 0.286 Chirality : 0.034 0.140 590 Planarity : 0.003 0.027 681 Dihedral : 3.181 17.824 521 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.95 % Allowed : 13.63 % Favored : 84.43 % 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: 6.03 (0.35), residues: 472 helix: 4.17 (0.22), residues: 435 sheet: None (None), residues: 0 loop : 0.32 (0.94), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 55 HIS 0.006 0.001 HIS A 41 PHE 0.027 0.002 PHE A 78 TYR 0.018 0.001 TYR B 242 ARG 0.003 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.7257 (t80) cc_final: 0.7037 (t80) REVERT: A 235 MET cc_start: 0.9072 (tpp) cc_final: 0.8452 (tmm) REVERT: B 125 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8592 (mp10) REVERT: B 235 MET cc_start: 0.8921 (tmm) cc_final: 0.8599 (tmm) REVERT: B 245 MET cc_start: 0.9158 (tpp) cc_final: 0.8922 (tpp) outliers start: 8 outliers final: 6 residues processed: 42 average time/residue: 0.1398 time to fit residues: 7.8803 Evaluate side-chains 44 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 0.0670 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.060868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.047876 restraints weight = 19293.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.049379 restraints weight = 8930.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.050357 restraints weight = 5457.648| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3891 Z= 0.185 Angle : 0.598 10.267 5235 Z= 0.301 Chirality : 0.034 0.155 590 Planarity : 0.003 0.026 681 Dihedral : 3.200 17.904 521 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.70 % Allowed : 13.87 % Favored : 84.43 % 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: 5.90 (0.35), residues: 472 helix: 4.08 (0.22), residues: 435 sheet: None (None), residues: 0 loop : 0.21 (0.95), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 55 HIS 0.008 0.002 HIS A 41 PHE 0.028 0.002 PHE A 78 TYR 0.030 0.002 TYR A 244 ARG 0.003 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.9017 (tpp) cc_final: 0.8457 (tmm) REVERT: B 103 ASP cc_start: 0.8788 (t0) cc_final: 0.8218 (t0) REVERT: B 125 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.8642 (mp10) REVERT: B 235 MET cc_start: 0.8906 (tmm) cc_final: 0.8583 (tmm) REVERT: B 245 MET cc_start: 0.9150 (tpp) cc_final: 0.8918 (tpp) outliers start: 7 outliers final: 6 residues processed: 43 average time/residue: 0.1471 time to fit residues: 8.6355 Evaluate side-chains 45 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS B 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.060011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.046999 restraints weight = 19344.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.048476 restraints weight = 8997.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.049412 restraints weight = 5535.733| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3891 Z= 0.216 Angle : 0.612 9.751 5235 Z= 0.313 Chirality : 0.034 0.123 590 Planarity : 0.003 0.026 681 Dihedral : 3.244 18.240 521 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.70 % Allowed : 14.11 % Favored : 84.18 % 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: 5.75 (0.35), residues: 472 helix: 3.98 (0.22), residues: 435 sheet: None (None), residues: 0 loop : 0.25 (0.96), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 55 HIS 0.011 0.002 HIS A 41 PHE 0.028 0.002 PHE A 78 TYR 0.041 0.002 TYR A 244 ARG 0.004 0.000 ARG A 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8255 (mmm) cc_final: 0.7985 (mmm) REVERT: A 235 MET cc_start: 0.9007 (tpp) cc_final: 0.8433 (tmm) REVERT: B 103 ASP cc_start: 0.8821 (t0) cc_final: 0.8255 (t0) REVERT: B 125 GLN cc_start: 0.9257 (OUTLIER) cc_final: 0.8687 (mp10) REVERT: B 235 MET cc_start: 0.8934 (tmm) cc_final: 0.8669 (tmm) REVERT: B 248 LEU cc_start: 0.8661 (tt) cc_final: 0.8418 (tt) outliers start: 7 outliers final: 6 residues processed: 40 average time/residue: 0.1374 time to fit residues: 7.3694 Evaluate side-chains 42 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 40 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.060257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.047015 restraints weight = 19217.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.048539 restraints weight = 8996.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.049544 restraints weight = 5581.891| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3891 Z= 0.189 Angle : 0.601 9.750 5235 Z= 0.305 Chirality : 0.034 0.126 590 Planarity : 0.003 0.026 681 Dihedral : 3.240 18.136 521 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.70 % Allowed : 13.87 % Favored : 84.43 % 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: 5.76 (0.35), residues: 472 helix: 4.00 (0.22), residues: 435 sheet: None (None), residues: 0 loop : 0.16 (0.94), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 55 HIS 0.006 0.001 HIS A 41 PHE 0.029 0.002 PHE A 78 TYR 0.022 0.002 TYR A 155 ARG 0.003 0.000 ARG A 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1546.87 seconds wall clock time: 27 minutes 46.88 seconds (1666.88 seconds total)