Starting phenix.real_space_refine on Mon Feb 10 20:39:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v4d_31708/02_2025/7v4d_31708.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v4d_31708/02_2025/7v4d_31708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v4d_31708/02_2025/7v4d_31708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v4d_31708/02_2025/7v4d_31708.map" model { file = "/net/cci-nas-00/data/ceres_data/7v4d_31708/02_2025/7v4d_31708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v4d_31708/02_2025/7v4d_31708.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1488 2.51 5 N 408 2.21 5 O 480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2376 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 396 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 1.67, per 1000 atoms: 0.70 Number of scatterers: 2376 At special positions: 0 Unit cell: (98.58, 87.98, 31.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 480 8.00 N 408 7.00 C 1488 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: 0.62 Conformation dependent library (CDL) restraints added in 339.5 milliseconds 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 588 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 43 through 44 removed outlier: 6.367A pdb=" N LYS F 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS C 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 48 through 50 Processing sheet with id=AA3, first strand: chain 'F' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'F' and resid 62 through 63 removed outlier: 6.128A pdb=" N GLN F 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN C 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 70 through 71 Processing sheet with id=AA6, first strand: chain 'F' and resid 81 through 82 Processing sheet with id=AA7, first strand: chain 'E' and resid 43 through 44 removed outlier: 6.361A pdb=" N LYS E 43 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LYS A 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 48 through 50 Processing sheet with id=AA9, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AB1, first strand: chain 'E' and resid 62 through 63 removed outlier: 6.129A pdb=" N GLN E 62 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLN A 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 70 through 71 Processing sheet with id=AB3, first strand: chain 'E' and resid 81 through 82 20 hydrogen bonds defined for protein. 60 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: 0.50 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 414 1.29 - 1.35: 373 1.35 - 1.42: 102 1.42 - 1.48: 401 1.48 - 1.55: 1098 Bond restraints: 2388 Sorted by residual: bond pdb=" CA LEU D 38 " pdb=" C LEU D 38 " ideal model delta sigma weight residual 1.523 1.533 -0.011 1.10e-02 8.26e+03 9.42e-01 bond pdb=" CA LEU F 38 " pdb=" C LEU F 38 " ideal model delta sigma weight residual 1.523 1.533 -0.011 1.10e-02 8.26e+03 9.17e-01 bond pdb=" CA LEU A 38 " pdb=" C LEU A 38 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 9.07e-01 bond pdb=" CA LEU E 38 " pdb=" C LEU E 38 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 9.04e-01 bond pdb=" CA LEU C 38 " pdb=" C LEU C 38 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 8.62e-01 ... (remaining 2383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.68: 2731 0.68 - 1.36: 401 1.36 - 2.04: 84 2.04 - 2.72: 18 2.72 - 3.41: 6 Bond angle restraints: 3240 Sorted by residual: angle pdb=" CA ASN B 65 " pdb=" CB ASN B 65 " pdb=" CG ASN B 65 " ideal model delta sigma weight residual 112.60 114.52 -1.92 1.00e+00 1.00e+00 3.70e+00 angle pdb=" CA ASN A 65 " pdb=" CB ASN A 65 " pdb=" CG ASN A 65 " ideal model delta sigma weight residual 112.60 114.49 -1.89 1.00e+00 1.00e+00 3.58e+00 angle pdb=" CA ASN E 65 " pdb=" CB ASN E 65 " pdb=" CG ASN E 65 " ideal model delta sigma weight residual 112.60 114.49 -1.89 1.00e+00 1.00e+00 3.58e+00 angle pdb=" CA ASN C 65 " pdb=" CB ASN C 65 " pdb=" CG ASN C 65 " ideal model delta sigma weight residual 112.60 114.48 -1.88 1.00e+00 1.00e+00 3.54e+00 angle pdb=" CA ASN F 65 " pdb=" CB ASN F 65 " pdb=" CG ASN F 65 " ideal model delta sigma weight residual 112.60 114.48 -1.88 1.00e+00 1.00e+00 3.52e+00 ... (remaining 3235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.21: 1206 12.21 - 24.43: 132 24.43 - 36.64: 18 36.64 - 48.85: 12 48.85 - 61.07: 6 Dihedral angle restraints: 1374 sinusoidal: 438 harmonic: 936 Sorted by residual: dihedral pdb=" CA VAL A 48 " pdb=" C VAL A 48 " pdb=" N VAL A 49 " pdb=" CA VAL A 49 " ideal model delta harmonic sigma weight residual 180.00 162.67 17.33 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA VAL B 48 " pdb=" C VAL B 48 " pdb=" N VAL B 49 " pdb=" CA VAL B 49 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA VAL C 48 " pdb=" C VAL C 48 " pdb=" N VAL C 49 " pdb=" CA VAL C 49 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 1371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 214 0.025 - 0.049: 108 0.049 - 0.074: 52 0.074 - 0.099: 34 0.099 - 0.124: 24 Chirality restraints: 432 Sorted by residual: chirality pdb=" CA VAL A 70 " pdb=" N VAL A 70 " pdb=" C VAL A 70 " pdb=" CB VAL A 70 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA VAL D 70 " pdb=" N VAL D 70 " pdb=" C VAL D 70 " pdb=" CB VAL D 70 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA VAL C 70 " pdb=" N VAL C 70 " pdb=" C VAL C 70 " pdb=" CB VAL C 70 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.62e-01 ... (remaining 429 not shown) Planarity restraints: 402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 87 " 0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" C SER C 87 " -0.020 2.00e-02 2.50e+03 pdb=" O SER C 87 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE C 88 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 87 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.29e+00 pdb=" C SER E 87 " 0.020 2.00e-02 2.50e+03 pdb=" O SER E 87 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE E 88 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 87 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.25e+00 pdb=" C SER F 87 " -0.019 2.00e-02 2.50e+03 pdb=" O SER F 87 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE F 88 " 0.006 2.00e-02 2.50e+03 ... (remaining 399 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 331 2.77 - 3.30: 2209 3.30 - 3.83: 3524 3.83 - 4.37: 3821 4.37 - 4.90: 7885 Nonbonded interactions: 17770 Sorted by model distance: nonbonded pdb=" OE1 GLU A 61 " pdb=" OG1 THR A 72 " model vdw 2.234 3.040 nonbonded pdb=" OE1 GLU E 61 " pdb=" OG1 THR E 72 " model vdw 2.235 3.040 nonbonded pdb=" OE1 GLU C 61 " pdb=" OG1 THR C 72 " model vdw 2.235 3.040 nonbonded pdb=" OE1 GLU B 61 " pdb=" OG1 THR B 72 " model vdw 2.235 3.040 nonbonded pdb=" OE1 GLU F 61 " pdb=" OG1 THR F 72 " model vdw 2.235 3.040 ... (remaining 17765 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 1.000 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.560 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 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 0.024 2388 Z= 0.196 Angle : 0.544 3.405 3240 Z= 0.315 Chirality : 0.045 0.124 432 Planarity : 0.002 0.011 402 Dihedral : 11.888 61.066 786 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.68 (0.26), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.32 (0.20), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 PHE 0.001 0.000 PHE F 94 TYR 0.002 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.258 Fit side-chains REVERT: F 83 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7835 (pm20) REVERT: C 46 GLU cc_start: 0.8223 (mt-10) cc_final: 0.8023 (mt-10) REVERT: C 83 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7843 (mm-30) REVERT: B 62 GLN cc_start: 0.8139 (tt0) cc_final: 0.7757 (tt0) REVERT: B 83 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7599 (mm-30) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0791 time to fit residues: 4.2168 Evaluate side-chains 35 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.4449 r_free = 0.4449 target = 0.164468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.135952 restraints weight = 2665.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.139270 restraints weight = 1365.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.141564 restraints weight = 948.262| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2388 Z= 0.332 Angle : 0.634 5.466 3240 Z= 0.346 Chirality : 0.047 0.134 432 Planarity : 0.003 0.012 402 Dihedral : 5.373 16.509 348 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 7.50 % Allowed : 12.92 % Favored : 79.58 % 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: -5.32 (0.29), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.22), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.005 0.001 PHE D 94 TYR 0.004 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.259 Fit side-chains REVERT: F 83 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7630 (pm20) REVERT: C 46 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7968 (mt-10) REVERT: C 83 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7883 (mm-30) REVERT: E 79 GLN cc_start: 0.8263 (mt0) cc_final: 0.7999 (mt0) outliers start: 18 outliers final: 11 residues processed: 52 average time/residue: 0.0767 time to fit residues: 5.4644 Evaluate side-chains 47 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.4497 r_free = 0.4497 target = 0.169102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.140431 restraints weight = 2599.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.143913 restraints weight = 1284.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.145983 restraints weight = 876.083| |-----------------------------------------------------------------------------| r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2388 Z= 0.309 Angle : 0.632 4.840 3240 Z= 0.349 Chirality : 0.047 0.137 432 Planarity : 0.003 0.014 402 Dihedral : 5.356 16.678 348 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 9.58 % Allowed : 15.83 % Favored : 74.58 % 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: -5.02 (0.31), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.24), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.004 0.001 PHE D 94 TYR 0.004 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 38 time to evaluate : 0.260 Fit side-chains REVERT: F 83 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7633 (pm20) REVERT: C 46 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7959 (mt-10) REVERT: C 83 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7965 (mm-30) outliers start: 23 outliers final: 20 residues processed: 52 average time/residue: 0.0697 time to fit residues: 5.0103 Evaluate side-chains 57 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 37 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.4428 r_free = 0.4428 target = 0.162843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.134339 restraints weight = 2667.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.137652 restraints weight = 1422.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.139901 restraints weight = 987.102| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 2388 Z= 0.457 Angle : 0.727 5.378 3240 Z= 0.397 Chirality : 0.048 0.142 432 Planarity : 0.003 0.014 402 Dihedral : 5.825 16.223 348 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 11.67 % Allowed : 12.50 % Favored : 75.83 % 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: -5.10 (0.32), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.24), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.007 0.001 PHE D 94 TYR 0.005 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 34 time to evaluate : 0.242 Fit side-chains REVERT: F 83 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7724 (pm20) REVERT: C 46 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8068 (mt-10) REVERT: C 83 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7953 (mm-30) REVERT: D 83 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7741 (mm-30) REVERT: B 62 GLN cc_start: 0.8271 (tt0) cc_final: 0.7934 (tt0) outliers start: 28 outliers final: 23 residues processed: 54 average time/residue: 0.0737 time to fit residues: 5.4269 Evaluate side-chains 56 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 33 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.170200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.143054 restraints weight = 2674.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.146407 restraints weight = 1374.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.148733 restraints weight = 941.862| |-----------------------------------------------------------------------------| r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2388 Z= 0.180 Angle : 0.592 6.745 3240 Z= 0.326 Chirality : 0.047 0.127 432 Planarity : 0.002 0.013 402 Dihedral : 5.032 15.958 348 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 7.08 % Allowed : 17.08 % Favored : 75.83 % 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: -4.59 (0.34), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.26), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.002 0.001 PHE D 94 TYR 0.002 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.293 Fit side-chains REVERT: F 83 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7755 (pm20) REVERT: C 46 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7974 (mt-10) outliers start: 17 outliers final: 14 residues processed: 49 average time/residue: 0.0719 time to fit residues: 4.8284 Evaluate side-chains 52 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.0570 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.165751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.138839 restraints weight = 2670.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.142232 restraints weight = 1386.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.144356 restraints weight = 948.481| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2388 Z= 0.278 Angle : 0.620 7.536 3240 Z= 0.336 Chirality : 0.046 0.132 432 Planarity : 0.003 0.019 402 Dihedral : 5.152 16.392 348 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 9.17 % Allowed : 15.00 % Favored : 75.83 % 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: -4.37 (0.35), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.004 0.001 PHE D 94 TYR 0.004 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 32 time to evaluate : 0.304 Fit side-chains REVERT: F 83 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7721 (pm20) REVERT: C 46 GLU cc_start: 0.8218 (mt-10) cc_final: 0.8000 (mt-10) outliers start: 22 outliers final: 18 residues processed: 47 average time/residue: 0.0780 time to fit residues: 5.0689 Evaluate side-chains 49 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 31 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4590 r_free = 0.4590 target = 0.171970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.144690 restraints weight = 2622.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.147940 restraints weight = 1302.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.150191 restraints weight = 883.086| |-----------------------------------------------------------------------------| r_work (final): 0.4355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2388 Z= 0.178 Angle : 0.590 6.809 3240 Z= 0.323 Chirality : 0.047 0.124 432 Planarity : 0.003 0.021 402 Dihedral : 4.791 15.798 348 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 8.33 % Allowed : 16.25 % Favored : 75.42 % 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: -4.05 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.003 0.001 PHE D 94 TYR 0.002 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 31 time to evaluate : 0.201 Fit side-chains REVERT: F 83 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7683 (pm20) REVERT: C 46 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7896 (mt-10) outliers start: 20 outliers final: 15 residues processed: 47 average time/residue: 0.0689 time to fit residues: 4.5049 Evaluate side-chains 46 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 31 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 HIS C 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.168055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.140847 restraints weight = 2765.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.144276 restraints weight = 1453.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.146392 restraints weight = 994.423| |-----------------------------------------------------------------------------| r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2388 Z= 0.305 Angle : 0.643 8.008 3240 Z= 0.346 Chirality : 0.047 0.131 432 Planarity : 0.003 0.020 402 Dihedral : 5.113 16.241 348 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 7.92 % Allowed : 13.75 % Favored : 78.33 % 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: -4.04 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.004 0.001 PHE D 94 TYR 0.005 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 29 time to evaluate : 0.242 Fit side-chains REVERT: C 46 GLU cc_start: 0.8230 (mt-10) cc_final: 0.8009 (mt-10) outliers start: 19 outliers final: 18 residues processed: 44 average time/residue: 0.0713 time to fit residues: 4.3310 Evaluate side-chains 47 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 29 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.175137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.147499 restraints weight = 2591.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.150905 restraints weight = 1267.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.153242 restraints weight = 855.620| |-----------------------------------------------------------------------------| r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2388 Z= 0.187 Angle : 0.595 7.550 3240 Z= 0.320 Chirality : 0.047 0.127 432 Planarity : 0.003 0.019 402 Dihedral : 4.746 15.525 348 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 6.67 % Allowed : 15.00 % Favored : 78.33 % 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: -3.79 (0.38), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.003 0.001 PHE D 94 TYR 0.002 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 0.228 Fit side-chains REVERT: C 46 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7948 (mt-10) outliers start: 16 outliers final: 16 residues processed: 45 average time/residue: 0.0745 time to fit residues: 4.6464 Evaluate side-chains 48 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 3.9990 chunk 25 optimal weight: 0.0870 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 0.4980 chunk 13 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- 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 = 0.4604 r_free = 0.4604 target = 0.170164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.143016 restraints weight = 2675.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.146314 restraints weight = 1393.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.148467 restraints weight = 960.753| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2388 Z= 0.263 Angle : 0.625 7.274 3240 Z= 0.336 Chirality : 0.046 0.129 432 Planarity : 0.003 0.019 402 Dihedral : 4.953 16.406 348 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 6.25 % Allowed : 15.42 % Favored : 78.33 % 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: -3.76 (0.38), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.004 0.001 PHE E 94 TYR 0.004 0.001 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.268 Fit side-chains REVERT: C 46 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7981 (mt-10) outliers start: 15 outliers final: 15 residues processed: 42 average time/residue: 0.0748 time to fit residues: 4.3698 Evaluate side-chains 45 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.4614 r_free = 0.4614 target = 0.170886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.143701 restraints weight = 2681.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.147055 restraints weight = 1396.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.149068 restraints weight = 964.428| |-----------------------------------------------------------------------------| r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2388 Z= 0.253 Angle : 0.620 7.218 3240 Z= 0.333 Chirality : 0.046 0.129 432 Planarity : 0.003 0.019 402 Dihedral : 5.011 15.706 348 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 6.67 % Allowed : 15.42 % Favored : 77.92 % 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: -3.69 (0.38), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 50 PHE 0.004 0.001 PHE E 94 TYR 0.003 0.001 TYR E 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1130.52 seconds wall clock time: 20 minutes 58.01 seconds (1258.01 seconds total)