Starting phenix.real_space_refine on Wed Mar 5 23:32:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnw_27582/03_2025/8dnw_27582.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnw_27582/03_2025/8dnw_27582.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/cci-nas-00/data/ceres_data/8dnw_27582/03_2025/8dnw_27582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnw_27582/03_2025/8dnw_27582.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnw_27582/03_2025/8dnw_27582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnw_27582/03_2025/8dnw_27582.cif" } 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= 0.003 sd= 0.033 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 26 5.16 5 C 2689 2.51 5 N 647 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 4060 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 457 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 57} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 251 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "A" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3352 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 416} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 3.09, per 1000 atoms: 0.76 Number of scatterers: 4060 At special positions: 0 Unit cell: (95.55, 79.8, 77.7, 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 26 16.00 O 698 8.00 N 647 7.00 C 2689 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: 0.97 Conformation dependent library (CDL) restraints added in 527.1 milliseconds 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 968 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 3 sheets defined 76.9% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 66 Proline residue: B 60 - end of helix Processing helix chain 'C' and resid 69 through 96 removed outlier: 3.644A pdb=" N VAL C 73 " --> pdb=" O GLY C 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 27 through 46 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 75 through 79 removed outlier: 4.556A pdb=" N LEU A 79 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 98 Processing helix chain 'A' and resid 110 through 135 removed outlier: 4.312A pdb=" N GLY A 135 " --> pdb=" O TYR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 171 removed outlier: 5.999A pdb=" N ALA A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N GLY A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE A 147 " --> pdb=" O MET A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 197 removed outlier: 3.616A pdb=" N LEU A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 223 Processing helix chain 'A' and resid 228 through 235 Processing helix chain 'A' and resid 241 through 260 removed outlier: 3.578A pdb=" N LEU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 312 Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 357 through 383 removed outlier: 3.897A pdb=" N GLU A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 408 through 438 removed outlier: 3.557A pdb=" N GLU A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 443 through 467 Processing sheet with id=AA1, first strand: chain 'C' and resid 66 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 282 removed outlier: 3.932A pdb=" N GLY A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 267 " --> pdb=" O GLY A 277 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 924 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: 1.15 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1231 1.34 - 1.46: 964 1.46 - 1.58: 1908 1.58 - 1.70: 0 1.70 - 1.81: 43 Bond restraints: 4146 Sorted by residual: bond pdb=" CA ILE A 281 " pdb=" CB ILE A 281 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.12e+00 bond pdb=" CG GLU B 32 " pdb=" CD GLU B 32 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.42e-01 bond pdb=" CB GLU B 32 " pdb=" CG GLU B 32 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.79e-01 bond pdb=" CG1 ILE A 48 " pdb=" CD1 ILE A 48 " ideal model delta sigma weight residual 1.513 1.484 0.029 3.90e-02 6.57e+02 5.71e-01 bond pdb=" CA ILE A 441 " pdb=" CB ILE A 441 " ideal model delta sigma weight residual 1.537 1.528 0.009 1.25e-02 6.40e+03 5.65e-01 ... (remaining 4141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 5514 1.51 - 3.02: 80 3.02 - 4.53: 17 4.53 - 6.04: 6 6.04 - 7.55: 1 Bond angle restraints: 5618 Sorted by residual: angle pdb=" CB MET A 91 " pdb=" CG MET A 91 " pdb=" SD MET A 91 " ideal model delta sigma weight residual 112.70 105.15 7.55 3.00e+00 1.11e-01 6.33e+00 angle pdb=" CB GLU B 32 " pdb=" CG GLU B 32 " pdb=" CD GLU B 32 " ideal model delta sigma weight residual 112.60 116.42 -3.82 1.70e+00 3.46e-01 5.04e+00 angle pdb=" N VAL A 382 " pdb=" CA VAL A 382 " pdb=" C VAL A 382 " ideal model delta sigma weight residual 111.00 113.37 -2.37 1.09e+00 8.42e-01 4.74e+00 angle pdb=" N GLY A 442 " pdb=" CA GLY A 442 " pdb=" C GLY A 442 " ideal model delta sigma weight residual 115.27 112.28 2.99 1.41e+00 5.03e-01 4.49e+00 angle pdb=" C ILE A 90 " pdb=" N MET A 91 " pdb=" CA MET A 91 " ideal model delta sigma weight residual 121.14 117.56 3.58 1.75e+00 3.27e-01 4.18e+00 ... (remaining 5613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.19: 2133 13.19 - 26.37: 217 26.37 - 39.56: 73 39.56 - 52.75: 17 52.75 - 65.93: 3 Dihedral angle restraints: 2443 sinusoidal: 936 harmonic: 1507 Sorted by residual: dihedral pdb=" CA THR A 286 " pdb=" C THR A 286 " pdb=" N SER A 287 " pdb=" CA SER A 287 " ideal model delta harmonic sigma weight residual -180.00 -164.08 -15.92 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ASN A 241 " pdb=" C ASN A 241 " pdb=" N LEU A 242 " pdb=" CA LEU A 242 " ideal model delta harmonic sigma weight residual 180.00 165.48 14.52 0 5.00e+00 4.00e-02 8.43e+00 dihedral pdb=" CB LYS A 392 " pdb=" CG LYS A 392 " pdb=" CD LYS A 392 " pdb=" CE LYS A 392 " ideal model delta sinusoidal sigma weight residual 60.00 105.11 -45.11 3 1.50e+01 4.44e-03 8.11e+00 ... (remaining 2440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 423 0.031 - 0.062: 173 0.062 - 0.092: 56 0.092 - 0.123: 15 0.123 - 0.154: 2 Chirality restraints: 669 Sorted by residual: chirality pdb=" CA MET A 91 " pdb=" N MET A 91 " pdb=" C MET A 91 " pdb=" CB MET A 91 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA ILE A 48 " pdb=" N ILE A 48 " pdb=" C ILE A 48 " pdb=" CB ILE A 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE A 281 " pdb=" N ILE A 281 " pdb=" C ILE A 281 " pdb=" CB ILE A 281 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 ... (remaining 666 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 9 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO B 10 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 10 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 10 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 239 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO A 240 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 240 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 240 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 71 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO C 72 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 72 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 72 " 0.021 5.00e-02 4.00e+02 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 13 2.56 - 3.15: 3351 3.15 - 3.73: 6573 3.73 - 4.32: 8301 4.32 - 4.90: 14462 Nonbonded interactions: 32700 Sorted by model distance: nonbonded pdb=" OE1 GLU A 78 " pdb=" OH TYR A 137 " model vdw 1.976 3.040 nonbonded pdb=" OD2 ASP A 139 " pdb=" OG SER A 141 " model vdw 2.152 3.040 nonbonded pdb=" OG1 THR B 26 " pdb=" OE2 GLU A 264 " model vdw 2.252 3.040 nonbonded pdb=" O VAL A 130 " pdb=" OG1 THR A 134 " model vdw 2.256 3.040 nonbonded pdb=" N THR A 323 " pdb=" O GLY A 339 " model vdw 2.358 3.120 ... (remaining 32695 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.260 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.480 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 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 : 0.003 0.029 4146 Z= 0.193 Angle : 0.515 7.549 5618 Z= 0.269 Chirality : 0.038 0.154 669 Planarity : 0.004 0.052 687 Dihedral : 12.461 65.934 1475 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 2.85 (0.37), residues: 514 helix: 2.59 (0.26), residues: 384 sheet: -2.76 (1.69), residues: 7 loop : -0.12 (0.61), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.015 0.001 PHE C 85 TYR 0.006 0.001 TYR A 457 ARG 0.002 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.444 Fit side-chains REVERT: B 38 MET cc_start: 0.7454 (tmm) cc_final: 0.6989 (tmm) REVERT: C 76 MET cc_start: 0.7862 (ttp) cc_final: 0.7595 (ttm) REVERT: A 64 TRP cc_start: 0.8316 (m100) cc_final: 0.8110 (m100) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1275 time to fit residues: 10.5345 Evaluate side-chains 53 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.151523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123465 restraints weight = 5309.724| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.92 r_work: 0.3153 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4146 Z= 0.215 Angle : 0.512 7.240 5618 Z= 0.260 Chirality : 0.039 0.152 669 Planarity : 0.004 0.046 687 Dihedral : 3.620 15.756 557 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.15 % Allowed : 6.45 % Favored : 92.40 % 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: 2.93 (0.37), residues: 514 helix: 2.59 (0.25), residues: 388 sheet: -2.75 (1.65), residues: 7 loop : 0.04 (0.62), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.023 0.001 PHE A 156 TYR 0.008 0.001 TYR A 457 ARG 0.005 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.462 Fit side-chains REVERT: B 38 MET cc_start: 0.7686 (tmm) cc_final: 0.7084 (tmm) REVERT: C 76 MET cc_start: 0.8610 (ttp) cc_final: 0.8165 (ttm) REVERT: C 86 MET cc_start: 0.8096 (mmm) cc_final: 0.7825 (mmm) REVERT: A 139 ASP cc_start: 0.8206 (t0) cc_final: 0.7989 (t0) REVERT: A 149 LEU cc_start: 0.8619 (tt) cc_final: 0.8268 (tt) REVERT: A 324 TRP cc_start: 0.8253 (m100) cc_final: 0.8000 (m100) outliers start: 5 outliers final: 4 residues processed: 60 average time/residue: 0.1311 time to fit residues: 10.5435 Evaluate side-chains 59 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 406 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 0.0050 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.151970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.123984 restraints weight = 5211.107| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.90 r_work: 0.3169 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4146 Z= 0.179 Angle : 0.489 6.882 5618 Z= 0.242 Chirality : 0.038 0.137 669 Planarity : 0.004 0.042 687 Dihedral : 3.535 15.180 557 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.15 % Allowed : 8.53 % Favored : 90.32 % 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: 3.04 (0.37), residues: 514 helix: 2.68 (0.25), residues: 388 sheet: -2.83 (1.61), residues: 7 loop : 0.04 (0.61), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.019 0.001 PHE A 156 TYR 0.006 0.001 TYR A 457 ARG 0.002 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.456 Fit side-chains REVERT: B 38 MET cc_start: 0.7810 (tmm) cc_final: 0.7171 (tmm) REVERT: C 76 MET cc_start: 0.8601 (ttp) cc_final: 0.8240 (ttm) REVERT: C 86 MET cc_start: 0.8094 (mmm) cc_final: 0.7782 (mmm) REVERT: A 139 ASP cc_start: 0.8288 (t0) cc_final: 0.8001 (t0) REVERT: A 149 LEU cc_start: 0.8638 (tt) cc_final: 0.8279 (tt) REVERT: A 153 ILE cc_start: 0.8796 (mm) cc_final: 0.8571 (mm) REVERT: A 324 TRP cc_start: 0.8347 (m100) cc_final: 0.8054 (m100) outliers start: 5 outliers final: 3 residues processed: 60 average time/residue: 0.1282 time to fit residues: 10.4458 Evaluate side-chains 60 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 0.0870 chunk 42 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.0570 chunk 8 optimal weight: 0.9980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.151551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123342 restraints weight = 5303.139| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.92 r_work: 0.3197 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4146 Z= 0.170 Angle : 0.479 6.926 5618 Z= 0.238 Chirality : 0.038 0.136 669 Planarity : 0.004 0.040 687 Dihedral : 3.481 15.177 557 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.92 % Allowed : 10.83 % Favored : 88.25 % 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: 3.06 (0.37), residues: 514 helix: 2.68 (0.25), residues: 388 sheet: -2.92 (1.45), residues: 7 loop : 0.11 (0.62), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.001 0.001 HIS B 58 PHE 0.016 0.001 PHE A 156 TYR 0.007 0.001 TYR A 457 ARG 0.003 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.463 Fit side-chains REVERT: B 38 MET cc_start: 0.7832 (tmm) cc_final: 0.7187 (tmm) REVERT: C 76 MET cc_start: 0.8579 (ttp) cc_final: 0.8188 (ttm) REVERT: C 86 MET cc_start: 0.8127 (mmm) cc_final: 0.7796 (mmm) REVERT: A 139 ASP cc_start: 0.8317 (t0) cc_final: 0.8074 (t0) REVERT: A 149 LEU cc_start: 0.8622 (tt) cc_final: 0.8364 (tt) REVERT: A 153 ILE cc_start: 0.8811 (mm) cc_final: 0.8566 (mm) REVERT: A 324 TRP cc_start: 0.8463 (m100) cc_final: 0.8134 (m100) outliers start: 4 outliers final: 3 residues processed: 59 average time/residue: 0.1267 time to fit residues: 10.1376 Evaluate side-chains 63 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 41 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.151156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.122536 restraints weight = 5395.777| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.95 r_work: 0.3193 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4146 Z= 0.176 Angle : 0.484 7.973 5618 Z= 0.238 Chirality : 0.037 0.135 669 Planarity : 0.004 0.040 687 Dihedral : 3.467 15.348 557 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.61 % Allowed : 12.44 % Favored : 85.94 % 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: 3.15 (0.37), residues: 514 helix: 2.74 (0.25), residues: 388 sheet: -2.96 (1.29), residues: 7 loop : 0.18 (0.63), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.015 0.001 PHE A 156 TYR 0.005 0.001 TYR A 457 ARG 0.003 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.408 Fit side-chains REVERT: B 38 MET cc_start: 0.7835 (tmm) cc_final: 0.7188 (tmm) REVERT: C 76 MET cc_start: 0.8549 (ttp) cc_final: 0.8183 (ttm) REVERT: C 86 MET cc_start: 0.8159 (mmm) cc_final: 0.7807 (mmm) REVERT: A 139 ASP cc_start: 0.8340 (t0) cc_final: 0.8109 (t0) REVERT: A 149 LEU cc_start: 0.8638 (tt) cc_final: 0.8358 (tt) REVERT: A 153 ILE cc_start: 0.8818 (mm) cc_final: 0.8551 (mm) REVERT: A 186 ASN cc_start: 0.8003 (t0) cc_final: 0.7622 (t0) REVERT: A 324 TRP cc_start: 0.8469 (m100) cc_final: 0.8169 (m100) outliers start: 7 outliers final: 5 residues processed: 64 average time/residue: 0.1319 time to fit residues: 11.4888 Evaluate side-chains 64 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 34 optimal weight: 0.1980 chunk 17 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 0.0270 chunk 11 optimal weight: 0.8980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.150488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.122067 restraints weight = 5247.249| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.90 r_work: 0.3192 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4146 Z= 0.152 Angle : 0.475 8.428 5618 Z= 0.231 Chirality : 0.037 0.139 669 Planarity : 0.004 0.039 687 Dihedral : 3.426 15.012 557 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.38 % Allowed : 13.59 % Favored : 85.02 % 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: 3.27 (0.37), residues: 514 helix: 2.82 (0.25), residues: 388 sheet: -2.75 (1.32), residues: 7 loop : 0.21 (0.63), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.001 0.001 HIS B 58 PHE 0.014 0.001 PHE A 156 TYR 0.007 0.001 TYR A 457 ARG 0.003 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.451 Fit side-chains REVERT: B 38 MET cc_start: 0.7824 (tmm) cc_final: 0.7169 (tmm) REVERT: C 76 MET cc_start: 0.8553 (ttp) cc_final: 0.8208 (ttm) REVERT: C 86 MET cc_start: 0.8222 (mmm) cc_final: 0.7872 (mmm) REVERT: A 139 ASP cc_start: 0.8362 (t0) cc_final: 0.8113 (t0) REVERT: A 149 LEU cc_start: 0.8632 (tt) cc_final: 0.8315 (tt) REVERT: A 153 ILE cc_start: 0.8789 (mm) cc_final: 0.8514 (mm) REVERT: A 186 ASN cc_start: 0.8104 (t0) cc_final: 0.7746 (t0) REVERT: A 324 TRP cc_start: 0.8477 (m100) cc_final: 0.8163 (m100) outliers start: 6 outliers final: 4 residues processed: 60 average time/residue: 0.1381 time to fit residues: 11.3282 Evaluate side-chains 61 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.0070 chunk 31 optimal weight: 0.5980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.151503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122994 restraints weight = 5266.933| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.92 r_work: 0.3156 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4146 Z= 0.172 Angle : 0.496 9.525 5618 Z= 0.239 Chirality : 0.037 0.158 669 Planarity : 0.004 0.039 687 Dihedral : 3.426 15.426 557 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.38 % Allowed : 14.06 % Favored : 84.56 % 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: 3.30 (0.37), residues: 514 helix: 2.83 (0.25), residues: 388 sheet: -2.72 (1.37), residues: 7 loop : 0.26 (0.63), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.013 0.001 PHE A 156 TYR 0.006 0.001 TYR A 457 ARG 0.003 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.357 Fit side-chains REVERT: B 38 MET cc_start: 0.7790 (tmm) cc_final: 0.7138 (tmm) REVERT: C 76 MET cc_start: 0.8565 (ttp) cc_final: 0.8216 (ttm) REVERT: C 86 MET cc_start: 0.8245 (mmm) cc_final: 0.7984 (mmm) REVERT: A 139 ASP cc_start: 0.8398 (t0) cc_final: 0.8145 (t0) REVERT: A 149 LEU cc_start: 0.8632 (tt) cc_final: 0.8304 (tt) REVERT: A 153 ILE cc_start: 0.8776 (mm) cc_final: 0.8497 (mm) REVERT: A 186 ASN cc_start: 0.8047 (t0) cc_final: 0.7640 (t0) REVERT: A 324 TRP cc_start: 0.8503 (m100) cc_final: 0.8147 (m100) outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 0.1192 time to fit residues: 9.8896 Evaluate side-chains 64 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 0.0870 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.151751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123435 restraints weight = 5146.780| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.89 r_work: 0.3188 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4146 Z= 0.167 Angle : 0.504 10.628 5618 Z= 0.240 Chirality : 0.037 0.179 669 Planarity : 0.004 0.038 687 Dihedral : 3.432 15.363 557 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.38 % Allowed : 14.75 % Favored : 83.87 % 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: 3.34 (0.37), residues: 514 helix: 2.86 (0.25), residues: 388 sheet: -2.96 (1.40), residues: 7 loop : 0.31 (0.63), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.013 0.001 PHE A 156 TYR 0.007 0.001 TYR A 457 ARG 0.003 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.418 Fit side-chains REVERT: B 38 MET cc_start: 0.7868 (tmm) cc_final: 0.7209 (tmm) REVERT: C 76 MET cc_start: 0.8556 (ttp) cc_final: 0.8225 (ttm) REVERT: C 86 MET cc_start: 0.8248 (mmm) cc_final: 0.7976 (mmm) REVERT: A 139 ASP cc_start: 0.8359 (t0) cc_final: 0.8122 (t0) REVERT: A 149 LEU cc_start: 0.8628 (tt) cc_final: 0.8174 (tt) REVERT: A 153 ILE cc_start: 0.8803 (mm) cc_final: 0.8529 (mm) REVERT: A 186 ASN cc_start: 0.8053 (t0) cc_final: 0.7670 (t0) REVERT: A 324 TRP cc_start: 0.8491 (m100) cc_final: 0.8105 (m100) outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 0.1318 time to fit residues: 10.8572 Evaluate side-chains 64 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.149454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.120707 restraints weight = 5295.304| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.92 r_work: 0.3134 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4146 Z= 0.214 Angle : 0.530 11.007 5618 Z= 0.253 Chirality : 0.038 0.176 669 Planarity : 0.004 0.038 687 Dihedral : 3.491 15.939 557 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.15 % Allowed : 15.21 % Favored : 83.64 % 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: 3.26 (0.37), residues: 514 helix: 2.78 (0.25), residues: 388 sheet: -3.04 (1.40), residues: 7 loop : 0.36 (0.64), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.013 0.001 PHE A 156 TYR 0.007 0.001 TYR A 457 ARG 0.003 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.468 Fit side-chains REVERT: B 38 MET cc_start: 0.7848 (tmm) cc_final: 0.7179 (tmm) REVERT: C 76 MET cc_start: 0.8576 (ttp) cc_final: 0.8224 (ttm) REVERT: C 86 MET cc_start: 0.8274 (mmm) cc_final: 0.7988 (mmm) REVERT: A 139 ASP cc_start: 0.8416 (t0) cc_final: 0.8137 (t0) REVERT: A 149 LEU cc_start: 0.8670 (tt) cc_final: 0.8360 (tt) REVERT: A 153 ILE cc_start: 0.8775 (mm) cc_final: 0.8516 (mm) REVERT: A 186 ASN cc_start: 0.8069 (t0) cc_final: 0.7674 (t0) REVERT: A 324 TRP cc_start: 0.8551 (m100) cc_final: 0.8106 (m100) outliers start: 5 outliers final: 5 residues processed: 62 average time/residue: 0.1172 time to fit residues: 9.9721 Evaluate side-chains 63 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 0.0670 chunk 47 optimal weight: 0.3980 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 2 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.148903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.120082 restraints weight = 5306.930| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.91 r_work: 0.3163 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4146 Z= 0.156 Angle : 0.533 12.867 5618 Z= 0.248 Chirality : 0.038 0.207 669 Planarity : 0.004 0.038 687 Dihedral : 3.453 15.256 557 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.15 % Allowed : 15.44 % Favored : 83.41 % 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: 3.34 (0.37), residues: 514 helix: 2.84 (0.25), residues: 388 sheet: -3.11 (1.42), residues: 7 loop : 0.40 (0.64), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.001 0.001 HIS B 58 PHE 0.013 0.001 PHE A 156 TYR 0.006 0.001 TYR A 457 ARG 0.004 0.000 ARG B 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.666 Fit side-chains REVERT: B 38 MET cc_start: 0.7860 (tmm) cc_final: 0.7202 (tmm) REVERT: C 76 MET cc_start: 0.8553 (ttp) cc_final: 0.8218 (ttm) REVERT: C 86 MET cc_start: 0.8222 (mmm) cc_final: 0.7947 (mmm) REVERT: A 139 ASP cc_start: 0.8390 (t0) cc_final: 0.8121 (t0) REVERT: A 149 LEU cc_start: 0.8600 (tt) cc_final: 0.8290 (tt) REVERT: A 153 ILE cc_start: 0.8771 (mm) cc_final: 0.8497 (mm) REVERT: A 186 ASN cc_start: 0.8048 (t0) cc_final: 0.7664 (t0) REVERT: A 324 TRP cc_start: 0.8534 (m100) cc_final: 0.8084 (m100) outliers start: 5 outliers final: 5 residues processed: 60 average time/residue: 0.1866 time to fit residues: 16.0518 Evaluate side-chains 61 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.148236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.119354 restraints weight = 5279.175| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.91 r_work: 0.3135 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4146 Z= 0.260 Angle : 0.578 13.942 5618 Z= 0.274 Chirality : 0.040 0.214 669 Planarity : 0.004 0.039 687 Dihedral : 3.577 16.366 557 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.38 % Allowed : 15.44 % Favored : 83.18 % 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: 3.09 (0.37), residues: 514 helix: 2.63 (0.25), residues: 388 sheet: -3.15 (1.41), residues: 7 loop : 0.44 (0.65), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.003 0.001 HIS A 218 PHE 0.014 0.001 PHE A 252 TYR 0.007 0.001 TYR A 457 ARG 0.003 0.000 ARG B 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2827.25 seconds wall clock time: 50 minutes 29.91 seconds (3029.91 seconds total)