Starting phenix.real_space_refine on Tue Feb 11 00:14:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wee_32448/02_2025/7wee_32448.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wee_32448/02_2025/7wee_32448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wee_32448/02_2025/7wee_32448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wee_32448/02_2025/7wee_32448.map" model { file = "/net/cci-nas-00/data/ceres_data/7wee_32448/02_2025/7wee_32448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wee_32448/02_2025/7wee_32448.cif" } resolution = 4.0 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= 0.003 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 14 5.16 5 C 2139 2.51 5 N 560 2.21 5 O 637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3350 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 938 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 800 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Time building chain proxies: 2.99, per 1000 atoms: 0.89 Number of scatterers: 3350 At special positions: 0 Unit cell: (87.74, 66.34, 100.58, 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 14 16.00 O 637 8.00 N 560 7.00 C 2139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 91 " distance=2.04 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: 0.83 Conformation dependent library (CDL) restraints added in 440.4 milliseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 8 sheets defined 8.2% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.842A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 Processing helix chain 'E' and resid 405 through 407 No H-bonds generated for 'chain 'E' and resid 405 through 407' Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.911A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.727A pdb=" N THR H 92 " --> pdb=" O PRO H 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 86 Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.321A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.321A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS E 432 " --> pdb=" O LEU E 513 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.984A pdb=" N ALA H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG H 60 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.354A pdb=" N VAL L 11 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN L 40 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU L 49 " --> pdb=" O GLN L 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 24 97 hydrogen bonds defined for protein. 228 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: 0.90 Time building geometry restraints manager: 0.98 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: 1057 1.34 - 1.46: 864 1.46 - 1.58: 1503 1.58 - 1.69: 1 1.69 - 1.81: 16 Bond restraints: 3441 Sorted by residual: bond pdb=" CG PRO H 9 " pdb=" CD PRO H 9 " ideal model delta sigma weight residual 1.503 1.344 0.159 3.40e-02 8.65e+02 2.18e+01 bond pdb=" CB PRO H 9 " pdb=" CG PRO H 9 " ideal model delta sigma weight residual 1.492 1.672 -0.180 5.00e-02 4.00e+02 1.30e+01 bond pdb=" N PRO H 9 " pdb=" CD PRO H 9 " ideal model delta sigma weight residual 1.473 1.509 -0.036 1.40e-02 5.10e+03 6.63e+00 bond pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 1.469 1.448 0.021 1.28e-02 6.10e+03 2.71e+00 bond pdb=" CA ASN H 86 " pdb=" CB ASN H 86 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.61e-02 3.86e+03 8.50e-01 ... (remaining 3436 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 4664 3.22 - 6.45: 21 6.45 - 9.67: 2 9.67 - 12.90: 1 12.90 - 16.12: 2 Bond angle restraints: 4690 Sorted by residual: angle pdb=" CA PRO H 9 " pdb=" N PRO H 9 " pdb=" CD PRO H 9 " ideal model delta sigma weight residual 112.00 95.88 16.12 1.40e+00 5.10e-01 1.33e+02 angle pdb=" N PRO H 9 " pdb=" CD PRO H 9 " pdb=" CG PRO H 9 " ideal model delta sigma weight residual 103.20 91.07 12.13 1.50e+00 4.44e-01 6.54e+01 angle pdb=" N ILE E 418 " pdb=" CA ILE E 418 " pdb=" C ILE E 418 " ideal model delta sigma weight residual 113.53 108.95 4.58 9.80e-01 1.04e+00 2.19e+01 angle pdb=" CA PRO H 9 " pdb=" CB PRO H 9 " pdb=" CG PRO H 9 " ideal model delta sigma weight residual 104.50 96.01 8.49 1.90e+00 2.77e-01 2.00e+01 angle pdb=" N PRO H 9 " pdb=" CA PRO H 9 " pdb=" CB PRO H 9 " ideal model delta sigma weight residual 103.25 99.58 3.67 1.05e+00 9.07e-01 1.22e+01 ... (remaining 4685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.10: 1760 14.10 - 28.20: 193 28.20 - 42.29: 61 42.29 - 56.39: 12 56.39 - 70.49: 1 Dihedral angle restraints: 2027 sinusoidal: 782 harmonic: 1245 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 91 " pdb=" CB CYS L 91 " ideal model delta sinusoidal sigma weight residual 93.00 22.51 70.49 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 130.56 -37.56 1 1.00e+01 1.00e-02 1.99e+01 dihedral pdb=" CA LEU E 517 " pdb=" C LEU E 517 " pdb=" N LEU E 518 " pdb=" CA LEU E 518 " ideal model delta harmonic sigma weight residual 180.00 158.07 21.93 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 2024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 358 0.039 - 0.079: 114 0.079 - 0.118: 37 0.118 - 0.157: 6 0.157 - 0.197: 2 Chirality restraints: 517 Sorted by residual: chirality pdb=" CB THR E 333 " pdb=" CA THR E 333 " pdb=" OG1 THR E 333 " pdb=" CG2 THR E 333 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.68e-01 chirality pdb=" CA PRO H 9 " pdb=" N PRO H 9 " pdb=" C PRO H 9 " pdb=" CB PRO H 9 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA ASN H 86 " pdb=" N ASN H 86 " pdb=" C ASN H 86 " pdb=" CB ASN H 86 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 514 not shown) Planarity restraints: 600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 8 " 0.056 5.00e-02 4.00e+02 7.59e-02 9.21e+00 pdb=" N PRO H 9 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO H 9 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 9 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 88 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO H 89 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 89 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 89 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 490 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO E 491 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO E 491 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 491 " 0.019 5.00e-02 4.00e+02 ... (remaining 597 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 50 2.67 - 3.23: 3069 3.23 - 3.79: 4699 3.79 - 4.34: 6398 4.34 - 4.90: 10716 Nonbonded interactions: 24932 Sorted by model distance: nonbonded pdb=" OG1 THR L 95 " pdb=" O SER L 98 " model vdw 2.116 3.040 nonbonded pdb=" OG1 THR H 104 " pdb=" OD1 ASP H 107 " model vdw 2.212 3.040 nonbonded pdb=" OG SER E 349 " pdb=" O LEU E 452 " model vdw 2.266 3.040 nonbonded pdb=" OG SER L 70 " pdb=" OG1 THR L 73 " model vdw 2.276 3.040 nonbonded pdb=" OG SER H 7 " pdb=" OG1 THR H 21 " model vdw 2.285 3.040 ... (remaining 24927 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 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: 1.920 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.290 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.180 3441 Z= 0.345 Angle : 0.720 16.124 4690 Z= 0.408 Chirality : 0.044 0.197 517 Planarity : 0.005 0.076 600 Dihedral : 12.682 54.785 1217 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.40), residues: 423 helix: -3.73 (0.83), residues: 21 sheet: -0.23 (0.42), residues: 141 loop : -1.33 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 HIS 0.005 0.001 HIS L 41 PHE 0.011 0.001 PHE L 65 TYR 0.011 0.001 TYR E 501 ARG 0.005 0.000 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7649 (p0) cc_final: 0.6915 (p0) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1074 time to fit residues: 9.2353 Evaluate side-chains 52 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.126501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 118)---------------| | r_work = 0.3289 r_free = 0.3289 target = 0.094609 restraints weight = 6964.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 93)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.089368 restraints weight = 8471.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.090129 restraints weight = 6364.321| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 3441 Z= 0.407 Angle : 0.694 8.465 4690 Z= 0.368 Chirality : 0.048 0.149 517 Planarity : 0.005 0.050 600 Dihedral : 5.436 26.740 470 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 1.62 % Allowed : 11.86 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.41), residues: 423 helix: -3.45 (0.85), residues: 26 sheet: -0.18 (0.40), residues: 152 loop : -1.38 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 436 HIS 0.002 0.001 HIS L 100 PHE 0.017 0.002 PHE E 429 TYR 0.015 0.002 TYR L 52 ARG 0.002 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.510 Fit side-chains REVERT: E 389 ASP cc_start: 0.7843 (p0) cc_final: 0.7256 (p0) REVERT: E 474 GLN cc_start: 0.7343 (pp30) cc_final: 0.6962 (pp30) REVERT: H 45 LYS cc_start: 0.8686 (ptmm) cc_final: 0.8294 (ptmm) REVERT: H 84 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7858 (tmm) REVERT: L 108 LYS cc_start: 0.7938 (tppt) cc_final: 0.7523 (tptt) outliers start: 6 outliers final: 4 residues processed: 54 average time/residue: 0.1417 time to fit residues: 9.7482 Evaluate side-chains 54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 6.9990 chunk 26 optimal weight: 0.0370 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 0.0070 overall best weight: 0.5276 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.131277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.104305 restraints weight = 6820.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.102676 restraints weight = 12744.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.104238 restraints weight = 10173.881| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 3441 Z= 0.158 Angle : 0.574 7.212 4690 Z= 0.296 Chirality : 0.043 0.142 517 Planarity : 0.004 0.051 600 Dihedral : 4.823 25.247 470 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.08 % Allowed : 16.17 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.41), residues: 423 helix: -3.51 (0.93), residues: 20 sheet: -0.08 (0.40), residues: 153 loop : -1.17 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 436 HIS 0.001 0.000 HIS L 41 PHE 0.014 0.001 PHE L 103 TYR 0.013 0.001 TYR E 380 ARG 0.002 0.000 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7764 (p0) cc_final: 0.7197 (p0) REVERT: H 45 LYS cc_start: 0.8178 (ptmm) cc_final: 0.7874 (ptmm) REVERT: L 108 LYS cc_start: 0.8016 (tppt) cc_final: 0.7800 (tptp) outliers start: 4 outliers final: 4 residues processed: 60 average time/residue: 0.1092 time to fit residues: 8.7531 Evaluate side-chains 57 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 22 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.127773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.102923 restraints weight = 7007.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.097582 restraints weight = 9694.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.095383 restraints weight = 9974.213| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3441 Z= 0.273 Angle : 0.615 6.209 4690 Z= 0.325 Chirality : 0.045 0.151 517 Planarity : 0.005 0.057 600 Dihedral : 5.189 26.206 470 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.23 % Allowed : 16.71 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.41), residues: 423 helix: -3.56 (0.81), residues: 27 sheet: -0.01 (0.40), residues: 150 loop : -1.27 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 55 HIS 0.002 0.001 HIS L 42 PHE 0.011 0.002 PHE L 65 TYR 0.011 0.002 TYR L 52 ARG 0.002 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.8103 (p0) cc_final: 0.7642 (p0) REVERT: E 474 GLN cc_start: 0.7180 (pp30) cc_final: 0.6803 (pp30) REVERT: L 103 PHE cc_start: 0.3880 (OUTLIER) cc_final: 0.3304 (m-10) outliers start: 12 outliers final: 9 residues processed: 64 average time/residue: 0.1144 time to fit residues: 9.6636 Evaluate side-chains 70 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 0.0970 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.129290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.097342 restraints weight = 6891.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.092369 restraints weight = 8237.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.093330 restraints weight = 6256.934| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3441 Z= 0.186 Angle : 0.591 7.630 4690 Z= 0.305 Chirality : 0.044 0.160 517 Planarity : 0.005 0.058 600 Dihedral : 4.959 25.409 470 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.50 % Allowed : 19.68 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.41), residues: 423 helix: -3.49 (0.81), residues: 26 sheet: -0.01 (0.40), residues: 153 loop : -1.21 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 109 HIS 0.001 0.000 HIS H 100 PHE 0.009 0.001 PHE H 24 TYR 0.009 0.001 TYR L 52 ARG 0.001 0.000 ARG E 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7821 (p0) cc_final: 0.7341 (p0) REVERT: E 474 GLN cc_start: 0.7188 (pp30) cc_final: 0.6748 (pp30) REVERT: L 103 PHE cc_start: 0.4240 (OUTLIER) cc_final: 0.3695 (m-10) outliers start: 13 outliers final: 9 residues processed: 68 average time/residue: 0.1086 time to fit residues: 9.7586 Evaluate side-chains 63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 30.0000 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.128972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.097871 restraints weight = 6981.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.096465 restraints weight = 9060.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.095893 restraints weight = 8034.085| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3441 Z= 0.199 Angle : 0.621 9.924 4690 Z= 0.310 Chirality : 0.044 0.166 517 Planarity : 0.004 0.054 600 Dihedral : 4.944 23.492 470 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.23 % Allowed : 22.64 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.41), residues: 423 helix: -3.50 (0.80), residues: 26 sheet: 0.02 (0.41), residues: 153 loop : -1.19 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 HIS 0.001 0.001 HIS L 42 PHE 0.010 0.001 PHE H 24 TYR 0.009 0.001 TYR H 96 ARG 0.001 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7903 (p0) cc_final: 0.7362 (p0) REVERT: E 474 GLN cc_start: 0.7120 (pp30) cc_final: 0.6680 (pp30) REVERT: L 103 PHE cc_start: 0.3734 (OUTLIER) cc_final: 0.3245 (m-10) outliers start: 12 outliers final: 9 residues processed: 69 average time/residue: 0.1097 time to fit residues: 10.0870 Evaluate side-chains 66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 0.0270 chunk 5 optimal weight: 0.3980 chunk 32 optimal weight: 9.9990 chunk 25 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.131367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.098982 restraints weight = 6834.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.094138 restraints weight = 7932.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.094969 restraints weight = 6019.167| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3441 Z= 0.143 Angle : 0.584 8.255 4690 Z= 0.292 Chirality : 0.043 0.163 517 Planarity : 0.004 0.055 600 Dihedral : 4.676 22.199 470 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.70 % Allowed : 22.91 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.41), residues: 423 helix: -3.83 (0.65), residues: 32 sheet: 0.19 (0.41), residues: 149 loop : -1.12 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 HIS 0.002 0.000 HIS L 42 PHE 0.011 0.001 PHE H 24 TYR 0.012 0.001 TYR E 501 ARG 0.001 0.000 ARG L 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7795 (p0) cc_final: 0.7286 (p0) REVERT: E 410 ILE cc_start: 0.8603 (mm) cc_final: 0.8342 (mm) REVERT: E 474 GLN cc_start: 0.6918 (pp30) cc_final: 0.6625 (pp30) REVERT: L 103 PHE cc_start: 0.3816 (OUTLIER) cc_final: 0.3188 (m-10) outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.0947 time to fit residues: 8.3081 Evaluate side-chains 62 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.130272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.098075 restraints weight = 6936.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.093226 restraints weight = 7829.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.094078 restraints weight = 6016.768| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3441 Z= 0.172 Angle : 0.587 8.199 4690 Z= 0.298 Chirality : 0.043 0.170 517 Planarity : 0.004 0.051 600 Dihedral : 4.677 21.507 470 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.70 % Allowed : 22.91 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.41), residues: 423 helix: -3.45 (0.79), residues: 26 sheet: 0.23 (0.41), residues: 149 loop : -1.28 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 HIS 0.001 0.000 HIS L 42 PHE 0.009 0.001 PHE H 24 TYR 0.008 0.001 TYR L 52 ARG 0.001 0.000 ARG H 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7804 (p0) cc_final: 0.7289 (p0) REVERT: E 474 GLN cc_start: 0.7015 (pp30) cc_final: 0.6560 (pp30) REVERT: L 103 PHE cc_start: 0.3812 (OUTLIER) cc_final: 0.3190 (m-10) outliers start: 10 outliers final: 8 residues processed: 65 average time/residue: 0.0997 time to fit residues: 8.8204 Evaluate side-chains 65 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.131079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 131)---------------| | r_work = 0.3347 r_free = 0.3347 target = 0.097771 restraints weight = 6824.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.094550 restraints weight = 6935.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.095285 restraints weight = 5477.472| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3441 Z= 0.158 Angle : 0.589 8.052 4690 Z= 0.298 Chirality : 0.044 0.192 517 Planarity : 0.004 0.049 600 Dihedral : 4.655 22.210 470 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.70 % Allowed : 22.91 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.41), residues: 423 helix: -3.82 (0.66), residues: 32 sheet: 0.26 (0.41), residues: 151 loop : -1.11 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 HIS 0.001 0.000 HIS L 42 PHE 0.012 0.001 PHE H 24 TYR 0.007 0.001 TYR L 52 ARG 0.001 0.000 ARG H 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7787 (p0) cc_final: 0.7281 (p0) REVERT: E 410 ILE cc_start: 0.8600 (mm) cc_final: 0.8321 (mm) REVERT: E 474 GLN cc_start: 0.6841 (pp30) cc_final: 0.6586 (pp30) REVERT: L 103 PHE cc_start: 0.3783 (OUTLIER) cc_final: 0.3058 (m-10) outliers start: 10 outliers final: 8 residues processed: 62 average time/residue: 0.1005 time to fit residues: 8.7367 Evaluate side-chains 63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 40 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.130711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.099407 restraints weight = 6831.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.098137 restraints weight = 8419.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.097388 restraints weight = 7285.716| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3441 Z= 0.166 Angle : 0.590 7.962 4690 Z= 0.299 Chirality : 0.044 0.191 517 Planarity : 0.004 0.049 600 Dihedral : 4.680 21.517 470 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.43 % Allowed : 23.45 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.41), residues: 423 helix: -3.42 (0.79), residues: 26 sheet: 0.30 (0.42), residues: 145 loop : -1.21 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 436 HIS 0.001 0.000 HIS E 519 PHE 0.009 0.001 PHE H 24 TYR 0.009 0.001 TYR L 52 ARG 0.001 0.000 ARG H 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7760 (p0) cc_final: 0.7251 (p0) REVERT: E 474 GLN cc_start: 0.6840 (pp30) cc_final: 0.6434 (pp30) REVERT: L 103 PHE cc_start: 0.3589 (OUTLIER) cc_final: 0.2712 (m-10) outliers start: 9 outliers final: 8 residues processed: 61 average time/residue: 0.1044 time to fit residues: 8.7067 Evaluate side-chains 64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 13 optimal weight: 0.0570 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.128116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.095399 restraints weight = 6915.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.094200 restraints weight = 8359.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.093525 restraints weight = 6150.352| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 0.027 3441 Z= 0.242 Angle : 0.634 7.993 4690 Z= 0.323 Chirality : 0.045 0.182 517 Planarity : 0.004 0.049 600 Dihedral : 5.075 23.637 470 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.43 % Allowed : 23.99 % Favored : 73.58 % 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: -1.24 (0.41), residues: 423 helix: -3.68 (0.86), residues: 20 sheet: 0.28 (0.42), residues: 145 loop : -1.29 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 436 HIS 0.001 0.001 HIS H 100 PHE 0.009 0.001 PHE E 429 TYR 0.013 0.001 TYR L 52 ARG 0.002 0.000 ARG E 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1537.59 seconds wall clock time: 28 minutes 18.52 seconds (1698.52 seconds total)