Starting phenix.real_space_refine on Tue Mar 11 21:55:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sj1_25152/03_2025/7sj1_25152.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sj1_25152/03_2025/7sj1_25152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sj1_25152/03_2025/7sj1_25152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sj1_25152/03_2025/7sj1_25152.map" model { file = "/net/cci-nas-00/data/ceres_data/7sj1_25152/03_2025/7sj1_25152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sj1_25152/03_2025/7sj1_25152.cif" } resolution = 2.9 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: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 28 5.16 5 C 4456 2.51 5 N 956 2.21 5 O 1021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6463 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1527 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1527 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1527 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1527 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 90 Unusual residues: {' K': 2, 'POV': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 67 Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.39, per 1000 atoms: 0.68 Number of scatterers: 6463 At special positions: 0 Unit cell: (95.46, 95.46, 64.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 28 16.00 O 1021 8.00 N 956 7.00 C 4456 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 792.4 milliseconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1480 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 86.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 226 through 247 Processing helix chain 'A' and resid 279 through 298 Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 320 through 326 Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 369 through 378 Processing helix chain 'A' and resid 380 through 392 Processing helix chain 'A' and resid 392 through 418 Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 452 through 472 Processing helix chain 'A' and resid 473 through 489 removed outlier: 4.374A pdb=" N ILE A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 247 Processing helix chain 'B' and resid 279 through 298 Processing helix chain 'B' and resid 311 through 319 Processing helix chain 'B' and resid 320 through 326 Processing helix chain 'B' and resid 358 through 368 Processing helix chain 'B' and resid 369 through 378 Processing helix chain 'B' and resid 380 through 392 Processing helix chain 'B' and resid 392 through 418 Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 441 Processing helix chain 'B' and resid 452 through 472 Processing helix chain 'B' and resid 473 through 489 removed outlier: 4.375A pdb=" N ILE B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 247 Processing helix chain 'C' and resid 279 through 298 Processing helix chain 'C' and resid 311 through 319 Processing helix chain 'C' and resid 320 through 326 Processing helix chain 'C' and resid 358 through 368 Processing helix chain 'C' and resid 369 through 378 Processing helix chain 'C' and resid 380 through 392 Processing helix chain 'C' and resid 392 through 418 Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 441 Processing helix chain 'C' and resid 452 through 472 Processing helix chain 'C' and resid 473 through 489 removed outlier: 4.375A pdb=" N ILE C 477 " --> pdb=" O PRO C 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 247 Processing helix chain 'D' and resid 279 through 298 Processing helix chain 'D' and resid 311 through 319 Processing helix chain 'D' and resid 320 through 326 Processing helix chain 'D' and resid 358 through 368 Processing helix chain 'D' and resid 369 through 378 Processing helix chain 'D' and resid 380 through 392 Processing helix chain 'D' and resid 392 through 418 Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 441 Processing helix chain 'D' and resid 452 through 472 Processing helix chain 'D' and resid 473 through 489 removed outlier: 4.374A pdb=" N ILE D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) 489 hydrogen bonds defined for protein. 1383 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.58 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 888 1.31 - 1.44: 1768 1.44 - 1.56: 3799 1.56 - 1.68: 69 1.68 - 1.81: 44 Bond restraints: 6568 Sorted by residual: bond pdb=" C21 POV C 706 " pdb=" O22 POV C 706 " ideal model delta sigma weight residual 1.205 1.415 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C21 POV B 707 " pdb=" O22 POV B 707 " ideal model delta sigma weight residual 1.205 1.414 -0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C21 POV A 705 " pdb=" O22 POV A 705 " ideal model delta sigma weight residual 1.205 1.414 -0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C21 POV D 708 " pdb=" O22 POV D 708 " ideal model delta sigma weight residual 1.205 1.414 -0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C21 POV A 705 " pdb=" O21 POV A 705 " ideal model delta sigma weight residual 1.330 1.199 0.131 2.00e-02 2.50e+03 4.31e+01 ... (remaining 6563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 8437 1.97 - 3.94: 180 3.94 - 5.91: 151 5.91 - 7.88: 16 7.88 - 9.85: 20 Bond angle restraints: 8804 Sorted by residual: angle pdb=" C THR B 449 " pdb=" N PRO B 450 " pdb=" CA PRO B 450 " ideal model delta sigma weight residual 119.56 115.15 4.41 1.02e+00 9.61e-01 1.87e+01 angle pdb=" C THR D 449 " pdb=" N PRO D 450 " pdb=" CA PRO D 450 " ideal model delta sigma weight residual 119.56 115.16 4.40 1.02e+00 9.61e-01 1.86e+01 angle pdb=" C THR A 449 " pdb=" N PRO A 450 " pdb=" CA PRO A 450 " ideal model delta sigma weight residual 119.56 115.18 4.38 1.02e+00 9.61e-01 1.84e+01 angle pdb=" C THR C 449 " pdb=" N PRO C 450 " pdb=" CA PRO C 450 " ideal model delta sigma weight residual 119.56 115.20 4.36 1.02e+00 9.61e-01 1.82e+01 angle pdb=" C32 POV B 708 " pdb=" C31 POV B 708 " pdb=" O31 POV B 708 " ideal model delta sigma weight residual 110.66 120.51 -9.85 3.00e+00 1.11e-01 1.08e+01 ... (remaining 8799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.19: 3548 24.19 - 48.38: 232 48.38 - 72.57: 52 72.57 - 96.76: 0 96.76 - 120.95: 4 Dihedral angle restraints: 3836 sinusoidal: 1568 harmonic: 2268 Sorted by residual: dihedral pdb=" C3 POV B 703 " pdb=" C31 POV B 703 " pdb=" O31 POV B 703 " pdb=" C32 POV B 703 " ideal model delta sinusoidal sigma weight residual 172.61 51.66 120.95 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" C3 POV C 702 " pdb=" C31 POV C 702 " pdb=" O31 POV C 702 " pdb=" C32 POV C 702 " ideal model delta sinusoidal sigma weight residual 172.61 51.68 120.93 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" C3 POV A 701 " pdb=" C31 POV A 701 " pdb=" O31 POV A 701 " pdb=" C32 POV A 701 " ideal model delta sinusoidal sigma weight residual 172.61 51.69 120.92 1 3.00e+01 1.11e-03 1.61e+01 ... (remaining 3833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 645 0.029 - 0.057: 252 0.057 - 0.086: 125 0.086 - 0.114: 29 0.114 - 0.143: 21 Chirality restraints: 1072 Sorted by residual: chirality pdb=" CA THR C 449 " pdb=" N THR C 449 " pdb=" C THR C 449 " pdb=" CB THR C 449 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA THR D 449 " pdb=" N THR D 449 " pdb=" C THR D 449 " pdb=" CB THR D 449 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA THR B 449 " pdb=" N THR B 449 " pdb=" C THR B 449 " pdb=" CB THR B 449 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 1069 not shown) Planarity restraints: 1016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 433 " -0.013 2.00e-02 2.50e+03 1.27e-02 2.80e+00 pdb=" CG PHE A 433 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 433 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 433 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 433 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 433 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 433 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 433 " -0.013 2.00e-02 2.50e+03 1.26e-02 2.78e+00 pdb=" CG PHE B 433 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE B 433 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 433 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 433 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 433 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 433 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 433 " -0.013 2.00e-02 2.50e+03 1.25e-02 2.72e+00 pdb=" CG PHE C 433 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 433 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 433 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 433 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 433 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 433 " 0.000 2.00e-02 2.50e+03 ... (remaining 1013 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.91: 2430 2.91 - 3.47: 7619 3.47 - 4.02: 10797 4.02 - 4.58: 16371 4.58 - 5.14: 22722 Nonbonded interactions: 59939 Sorted by model distance: nonbonded pdb=" O VAL B 407 " pdb=" OG SER B 411 " model vdw 2.351 3.040 nonbonded pdb=" O VAL A 407 " pdb=" OG SER A 411 " model vdw 2.351 3.040 nonbonded pdb=" O VAL D 407 " pdb=" OG SER D 411 " model vdw 2.351 3.040 nonbonded pdb=" O VAL C 407 " pdb=" OG SER C 411 " model vdw 2.351 3.040 nonbonded pdb=" O THR C 441 " pdb=" OG1 THR C 442 " model vdw 2.365 3.040 ... (remaining 59934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 226 through 489 or (resid 702 and (name C31 or name C32 or \ name C33 or name C34 or name C35)) or (resid 703 through 704 and (name C32 or n \ ame C33 or name C34 or name C35)))) selection = (chain 'B' and (resid 226 through 489 or (resid 702 and (name C31 or name C32 or \ name C33 or name C34 or name C35)) or (resid 703 through 704 and (name C32 or n \ ame C33 or name C34 or name C35)))) selection = (chain 'C' and (resid 226 through 489 or (resid 702 and (name C31 or name C32 or \ name C33 or name C34 or name C35)) or (resid 703 through 704 and (name C32 or n \ ame C33 or name C34 or name C35)))) selection = (chain 'D' and (resid 226 through 489 or (resid 702 and (name C31 or name C32 or \ name C33 or name C34 or name C35)) or (resid 703 through 704 and (name C32 or n \ ame C33 or name C34 or name C35)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.500 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 : 0.011 0.210 6568 Z= 0.731 Angle : 1.007 9.847 8804 Z= 0.418 Chirality : 0.041 0.143 1072 Planarity : 0.004 0.037 1016 Dihedral : 16.624 120.953 2356 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.61 % Allowed : 0.15 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.31), residues: 752 helix: 2.17 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.63 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 454 HIS 0.001 0.000 HIS B 486 PHE 0.029 0.002 PHE A 433 TYR 0.022 0.002 TYR D 485 ARG 0.002 0.000 ARG D 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 167 time to evaluate : 0.651 Fit side-chains REVERT: A 285 LEU cc_start: 0.7714 (mm) cc_final: 0.7489 (tp) REVERT: A 312 MET cc_start: 0.6708 (mtt) cc_final: 0.6090 (tpp) REVERT: A 485 TYR cc_start: 0.6842 (t80) cc_final: 0.6159 (t80) REVERT: B 285 LEU cc_start: 0.7702 (mm) cc_final: 0.7491 (tp) REVERT: B 312 MET cc_start: 0.6717 (mtt) cc_final: 0.6103 (tpp) REVERT: B 485 TYR cc_start: 0.6825 (t80) cc_final: 0.6178 (t80) REVERT: C 312 MET cc_start: 0.6700 (mtt) cc_final: 0.6162 (tpp) REVERT: C 485 TYR cc_start: 0.6837 (t80) cc_final: 0.6182 (t80) REVERT: D 312 MET cc_start: 0.6679 (mtt) cc_final: 0.6152 (tpp) REVERT: D 485 TYR cc_start: 0.6858 (t80) cc_final: 0.6268 (t80) outliers start: 4 outliers final: 0 residues processed: 171 average time/residue: 1.0841 time to fit residues: 194.9327 Evaluate side-chains 131 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 0.4980 chunk 19 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 0.0030 chunk 23 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.179526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.133377 restraints weight = 6745.508| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.23 r_work: 0.3407 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6568 Z= 0.214 Angle : 0.576 8.385 8804 Z= 0.299 Chirality : 0.040 0.131 1072 Planarity : 0.005 0.037 1016 Dihedral : 13.194 83.887 1060 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.06 % Allowed : 16.97 % Favored : 81.97 % 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: 3.35 (0.31), residues: 752 helix: 2.50 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 1.16 (0.63), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 435 HIS 0.002 0.001 HIS A 486 PHE 0.020 0.002 PHE D 433 TYR 0.014 0.002 TYR C 323 ARG 0.003 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.671 Fit side-chains REVERT: A 285 LEU cc_start: 0.7477 (mm) cc_final: 0.7110 (tp) REVERT: B 285 LEU cc_start: 0.7476 (mm) cc_final: 0.7097 (tp) REVERT: C 312 MET cc_start: 0.6259 (mtt) cc_final: 0.5790 (mmt) outliers start: 7 outliers final: 7 residues processed: 125 average time/residue: 1.2685 time to fit residues: 166.1174 Evaluate side-chains 123 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 393 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.173426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126900 restraints weight = 6609.825| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.39 r_work: 0.3412 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6568 Z= 0.206 Angle : 0.533 5.976 8804 Z= 0.276 Chirality : 0.039 0.126 1072 Planarity : 0.004 0.037 1016 Dihedral : 11.434 74.507 1060 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.42 % Allowed : 17.88 % Favored : 79.70 % 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: 3.41 (0.31), residues: 752 helix: 2.63 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.71 (0.59), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 289 HIS 0.002 0.001 HIS D 486 PHE 0.012 0.001 PHE C 433 TYR 0.008 0.001 TYR B 323 ARG 0.001 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.630 Fit side-chains REVERT: A 312 MET cc_start: 0.6399 (mtt) cc_final: 0.5829 (mmt) REVERT: B 284 THR cc_start: 0.8265 (m) cc_final: 0.8053 (p) REVERT: B 312 MET cc_start: 0.6406 (mtt) cc_final: 0.5945 (mmt) REVERT: C 284 THR cc_start: 0.8285 (m) cc_final: 0.8082 (p) REVERT: C 312 MET cc_start: 0.6329 (mtt) cc_final: 0.5935 (mmt) REVERT: C 407 VAL cc_start: 0.7982 (p) cc_final: 0.7768 (t) REVERT: D 312 MET cc_start: 0.6291 (mtt) cc_final: 0.5829 (mmt) REVERT: D 407 VAL cc_start: 0.7997 (p) cc_final: 0.7792 (t) outliers start: 16 outliers final: 1 residues processed: 128 average time/residue: 1.2163 time to fit residues: 163.2603 Evaluate side-chains 102 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 393 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 39 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 62 optimal weight: 0.0070 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.173925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127694 restraints weight = 6702.695| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.29 r_work: 0.3417 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6568 Z= 0.211 Angle : 0.542 8.492 8804 Z= 0.280 Chirality : 0.041 0.205 1072 Planarity : 0.004 0.035 1016 Dihedral : 10.405 66.494 1060 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.52 % Allowed : 20.30 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.49 (0.31), residues: 752 helix: 2.70 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.66 (0.59), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 289 HIS 0.001 0.001 HIS C 486 PHE 0.012 0.001 PHE A 433 TYR 0.013 0.001 TYR A 323 ARG 0.009 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.610 Fit side-chains REVERT: A 312 MET cc_start: 0.6192 (mtt) cc_final: 0.5934 (mmt) REVERT: B 312 MET cc_start: 0.6268 (mtt) cc_final: 0.5879 (mmt) REVERT: C 312 MET cc_start: 0.6189 (mtt) cc_final: 0.5876 (mmt) REVERT: D 312 MET cc_start: 0.6235 (mtt) cc_final: 0.5823 (mmt) outliers start: 10 outliers final: 1 residues processed: 122 average time/residue: 1.3258 time to fit residues: 168.7153 Evaluate side-chains 100 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 393 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 0.0010 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.174003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.128668 restraints weight = 6689.116| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.29 r_work: 0.3425 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6568 Z= 0.203 Angle : 0.542 12.212 8804 Z= 0.277 Chirality : 0.040 0.137 1072 Planarity : 0.005 0.037 1016 Dihedral : 9.546 60.831 1060 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.36 % Allowed : 21.06 % Favored : 77.58 % 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: 3.57 (0.31), residues: 752 helix: 2.77 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.61 (0.59), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 289 HIS 0.001 0.001 HIS D 486 PHE 0.012 0.001 PHE A 433 TYR 0.018 0.001 TYR D 485 ARG 0.010 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.721 Fit side-chains REVERT: A 281 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8182 (tm) REVERT: A 312 MET cc_start: 0.6180 (mtt) cc_final: 0.5847 (mmt) REVERT: B 281 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8261 (tm) REVERT: B 312 MET cc_start: 0.6131 (mtt) cc_final: 0.5827 (mmt) REVERT: D 312 MET cc_start: 0.6234 (mtt) cc_final: 0.5968 (mmt) outliers start: 9 outliers final: 1 residues processed: 111 average time/residue: 1.4881 time to fit residues: 171.9411 Evaluate side-chains 101 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 393 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 41 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 67 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4281 r_free = 0.4281 target = 0.184657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.142079 restraints weight = 6624.073| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.16 r_work: 0.3435 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6568 Z= 0.192 Angle : 0.542 12.459 8804 Z= 0.271 Chirality : 0.040 0.142 1072 Planarity : 0.004 0.037 1016 Dihedral : 8.657 55.312 1060 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.61 % Allowed : 22.12 % Favored : 77.27 % 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: 3.62 (0.31), residues: 752 helix: 2.80 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.63 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 289 HIS 0.002 0.001 HIS A 486 PHE 0.011 0.001 PHE D 433 TYR 0.019 0.001 TYR D 485 ARG 0.008 0.001 ARG D 487 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.710 Fit side-chains REVERT: A 312 MET cc_start: 0.6077 (mtt) cc_final: 0.5681 (mmt) REVERT: B 312 MET cc_start: 0.6040 (mtt) cc_final: 0.5771 (mmt) REVERT: D 312 MET cc_start: 0.6110 (mtt) cc_final: 0.5728 (mmt) REVERT: D 324 PHE cc_start: 0.6713 (m-80) cc_final: 0.6451 (m-80) outliers start: 4 outliers final: 1 residues processed: 117 average time/residue: 1.3466 time to fit residues: 164.6862 Evaluate side-chains 105 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 393 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 18 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.170830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.123241 restraints weight = 6738.470| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.18 r_work: 0.3377 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6568 Z= 0.253 Angle : 0.612 14.200 8804 Z= 0.309 Chirality : 0.043 0.145 1072 Planarity : 0.004 0.034 1016 Dihedral : 8.625 52.232 1060 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.82 % Allowed : 21.82 % Favored : 76.36 % 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: 3.51 (0.31), residues: 752 helix: 2.70 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.74 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 289 HIS 0.003 0.001 HIS D 486 PHE 0.030 0.002 PHE D 481 TYR 0.020 0.002 TYR D 485 ARG 0.007 0.001 ARG B 377 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.689 Fit side-chains REVERT: A 312 MET cc_start: 0.6191 (mtt) cc_final: 0.5791 (mmt) REVERT: B 312 MET cc_start: 0.6156 (mtt) cc_final: 0.5784 (mmt) outliers start: 12 outliers final: 1 residues processed: 125 average time/residue: 1.2518 time to fit residues: 163.9631 Evaluate side-chains 115 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 393 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.3980 chunk 4 optimal weight: 3.9990 chunk 55 optimal weight: 0.0170 chunk 15 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.173204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.127024 restraints weight = 6806.931| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.35 r_work: 0.3403 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6568 Z= 0.216 Angle : 0.591 13.440 8804 Z= 0.297 Chirality : 0.041 0.139 1072 Planarity : 0.004 0.034 1016 Dihedral : 8.227 49.802 1060 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.36 % Allowed : 23.18 % Favored : 75.45 % 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: 3.59 (0.31), residues: 752 helix: 2.74 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.86 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 289 HIS 0.002 0.000 HIS C 486 PHE 0.023 0.001 PHE D 481 TYR 0.021 0.002 TYR B 485 ARG 0.007 0.000 ARG D 377 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.694 Fit side-chains REVERT: A 312 MET cc_start: 0.6078 (mtt) cc_final: 0.5709 (mmt) REVERT: B 312 MET cc_start: 0.6037 (mtt) cc_final: 0.5708 (mmt) REVERT: C 312 MET cc_start: 0.6288 (OUTLIER) cc_final: 0.4979 (mmm) outliers start: 9 outliers final: 1 residues processed: 127 average time/residue: 1.2319 time to fit residues: 164.0044 Evaluate side-chains 118 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain C residue 312 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 75 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4255 r_free = 0.4255 target = 0.182467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.138159 restraints weight = 6899.120| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.15 r_work: 0.3515 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6568 Z= 0.227 Angle : 0.606 14.095 8804 Z= 0.304 Chirality : 0.042 0.142 1072 Planarity : 0.004 0.034 1016 Dihedral : 8.064 52.940 1060 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.06 % Allowed : 23.64 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.58 (0.31), residues: 752 helix: 2.74 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.83 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 289 HIS 0.001 0.000 HIS B 486 PHE 0.022 0.001 PHE D 481 TYR 0.021 0.002 TYR D 485 ARG 0.008 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.648 Fit side-chains REVERT: A 312 MET cc_start: 0.6159 (mtt) cc_final: 0.5835 (mmt) REVERT: B 312 MET cc_start: 0.6083 (mtt) cc_final: 0.5787 (mmt) REVERT: C 312 MET cc_start: 0.6311 (OUTLIER) cc_final: 0.4992 (mmt) outliers start: 7 outliers final: 7 residues processed: 129 average time/residue: 1.2038 time to fit residues: 163.2356 Evaluate side-chains 126 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 486 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 69 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4255 r_free = 0.4255 target = 0.182930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.138693 restraints weight = 6871.747| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.12 r_work: 0.3585 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6568 Z= 0.215 Angle : 0.625 14.373 8804 Z= 0.308 Chirality : 0.041 0.147 1072 Planarity : 0.004 0.034 1016 Dihedral : 7.921 58.518 1060 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.76 % Allowed : 23.94 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.31), residues: 752 helix: 2.72 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.87 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 289 HIS 0.001 0.000 HIS C 486 PHE 0.028 0.001 PHE B 481 TYR 0.021 0.002 TYR D 485 ARG 0.007 0.000 ARG B 377 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.697 Fit side-chains REVERT: B 312 MET cc_start: 0.5979 (mtt) cc_final: 0.5774 (mmt) REVERT: D 312 MET cc_start: 0.6138 (mtt) cc_final: 0.5802 (mmt) outliers start: 5 outliers final: 4 residues processed: 121 average time/residue: 1.2510 time to fit residues: 158.9531 Evaluate side-chains 120 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain D residue 486 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.0570 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.4273 r_free = 0.4273 target = 0.184348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.140388 restraints weight = 6950.751| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.13 r_work: 0.3651 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6568 Z= 0.215 Angle : 0.631 14.513 8804 Z= 0.308 Chirality : 0.041 0.150 1072 Planarity : 0.004 0.034 1016 Dihedral : 7.545 54.541 1060 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.76 % Allowed : 24.70 % Favored : 74.55 % 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: 3.59 (0.31), residues: 752 helix: 2.75 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.79 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 289 HIS 0.000 0.000 HIS C 486 PHE 0.028 0.001 PHE B 481 TYR 0.021 0.002 TYR B 485 ARG 0.007 0.000 ARG A 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4783.69 seconds wall clock time: 82 minutes 18.57 seconds (4938.57 seconds total)