Starting phenix.real_space_refine on Tue Feb 13 22:11:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp8_25368/02_2024/7sp8_25368.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp8_25368/02_2024/7sp8_25368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp8_25368/02_2024/7sp8_25368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp8_25368/02_2024/7sp8_25368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp8_25368/02_2024/7sp8_25368.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp8_25368/02_2024/7sp8_25368.pdb" } resolution = 2.7 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= -0.001 sd= 0.791 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1820 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 3 5.49 5 S 35 5.16 5 C 3935 2.51 5 N 999 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 140": "OD1" <-> "OD2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6090 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4088 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 500, 4077 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 13, 'TRANS': 486} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 500, 4077 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 13, 'TRANS': 486} Chain breaks: 1 bond proxies already assigned to first conformer: 4176 Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 950 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "C" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 925 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 1 Chain: "A" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 127 Unusual residues: {' MN': 2, '3PE': 1, 'UD1': 1, 'Y01': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 303 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 303 " occ=0.50 Time building chain proxies: 5.73, per 1000 atoms: 0.94 Number of scatterers: 6090 At special positions: 0 Unit cell: (73.44, 72.36, 153.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 35 16.00 P 3 15.00 O 1116 8.00 N 999 7.00 C 3935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.30 Conformation dependent library (CDL) restraints added in 1.9 seconds 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1378 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 47.3% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 38 through 74 removed outlier: 3.648A pdb=" N LEU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.655A pdb=" N ALA A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.509A pdb=" N SER A 152 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 209 through 221 Proline residue: A 217 - end of helix removed outlier: 3.560A pdb=" N CYS A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 262 removed outlier: 4.051A pdb=" N ARG A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLY A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 5.221A pdb=" N ASP A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 331 through 357 removed outlier: 4.281A pdb=" N TRP A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 361 Processing helix chain 'A' and resid 364 through 392 Processing helix chain 'A' and resid 393 through 420 removed outlier: 3.507A pdb=" N GLN A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.707A pdb=" N ALA A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 428 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 449 removed outlier: 4.031A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix Processing helix chain 'A' and resid 468 through 497 removed outlier: 4.083A pdb=" N GLN A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 476 " --> pdb=" O TRP A 472 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N THR A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 535 Processing helix chain 'A' and resid 539 through 551 removed outlier: 3.750A pdb=" N LYS A 543 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.522A pdb=" N THR B 31 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'C' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143 removed outlier: 3.656A pdb=" N ILE A 168 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL A 84 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ILE A 117 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL A 86 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL A 119 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE A 88 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 89 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU A 272 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ILE A 224 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 10.639A pdb=" N TYR A 318 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N ALA A 226 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N ALA A 228 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA A 322 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501 removed outlier: 6.554A pdb=" N PHE A 500 " --> pdb=" O GLY B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.630A pdb=" N SER B 21 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 18 " --> pdb=" O MET B 82 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 20 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 13 removed outlier: 6.292A pdb=" N VAL B 12 " --> pdb=" O SER B 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 59 removed outlier: 5.877A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 92 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 59 removed outlier: 5.877A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 92 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.592A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 20 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 59 removed outlier: 6.050A pdb=" N PHE C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG C 38 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 34 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR C 93 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY C 119 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N CYS C 95 " --> pdb=" O GLY C 117 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 945 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: 1.75 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 942 1.31 - 1.43: 1856 1.43 - 1.56: 3363 1.56 - 1.69: 28 1.69 - 1.81: 53 Bond restraints: 6242 Sorted by residual: bond pdb=" C2B UD1 A 601 " pdb=" C3B UD1 A 601 " ideal model delta sigma weight residual 1.533 1.303 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C5 UD1 A 601 " pdb=" C6 UD1 A 601 " ideal model delta sigma weight residual 1.342 1.484 -0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" C2 UD1 A 601 " pdb=" N3 UD1 A 601 " ideal model delta sigma weight residual 1.371 1.501 -0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" CBD Y01 A 603 " pdb=" CBG Y01 A 603 " ideal model delta sigma weight residual 1.520 1.644 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C7' UD1 A 601 " pdb=" N2' UD1 A 601 " ideal model delta sigma weight residual 1.347 1.465 -0.118 2.00e-02 2.50e+03 3.49e+01 ... (remaining 6237 not shown) Histogram of bond angle deviations from ideal: 98.99 - 105.98: 97 105.98 - 112.98: 3298 112.98 - 119.98: 2147 119.98 - 126.97: 2853 126.97 - 133.97: 74 Bond angle restraints: 8469 Sorted by residual: angle pdb=" O1' UD1 A 601 " pdb=" PB UD1 A 601 " pdb=" O3A UD1 A 601 " ideal model delta sigma weight residual 92.88 109.25 -16.37 3.00e+00 1.11e-01 2.98e+01 angle pdb=" O3A UD1 A 601 " pdb=" PA UD1 A 601 " pdb=" O5B UD1 A 601 " ideal model delta sigma weight residual 94.40 109.61 -15.21 3.00e+00 1.11e-01 2.57e+01 angle pdb=" O12 3PE A 602 " pdb=" P 3PE A 602 " pdb=" O14 3PE A 602 " ideal model delta sigma weight residual 123.79 109.19 14.60 3.00e+00 1.11e-01 2.37e+01 angle pdb=" CAM Y01 A 603 " pdb=" CAY Y01 A 603 " pdb=" OAW Y01 A 603 " ideal model delta sigma weight residual 111.19 124.36 -13.17 3.00e+00 1.11e-01 1.93e+01 angle pdb=" CAI Y01 A 603 " pdb=" CAZ Y01 A 603 " pdb=" CAV Y01 A 603 " ideal model delta sigma weight residual 120.03 131.68 -11.65 3.00e+00 1.11e-01 1.51e+01 ... (remaining 8464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.02: 3558 28.02 - 56.04: 147 56.04 - 84.06: 19 84.06 - 112.08: 1 112.08 - 140.10: 1 Dihedral angle restraints: 3726 sinusoidal: 1560 harmonic: 2166 Sorted by residual: dihedral pdb=" O21 3PE A 602 " pdb=" C2 3PE A 602 " pdb=" C3 3PE A 602 " pdb=" O31 3PE A 602 " ideal model delta sinusoidal sigma weight residual 60.47 -159.43 -140.10 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" CA GLU A 548 " pdb=" C GLU A 548 " pdb=" N ARG A 549 " pdb=" CA ARG A 549 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ASP C 59 " pdb=" CB ASP C 59 " pdb=" CG ASP C 59 " pdb=" OD1 ASP C 59 " ideal model delta sinusoidal sigma weight residual -30.00 -84.64 54.64 1 2.00e+01 2.50e-03 1.01e+01 ... (remaining 3723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 844 0.079 - 0.158: 62 0.158 - 0.237: 8 0.237 - 0.316: 2 0.316 - 0.395: 3 Chirality restraints: 919 Sorted by residual: chirality pdb=" CBG Y01 A 603 " pdb=" CAQ Y01 A 603 " pdb=" CBD Y01 A 603 " pdb=" CBI Y01 A 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CBE Y01 A 603 " pdb=" CAP Y01 A 603 " pdb=" CBB Y01 A 603 " pdb=" CBI Y01 A 603 " both_signs ideal model delta sigma weight residual False 2.57 2.93 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CBI Y01 A 603 " pdb=" CAU Y01 A 603 " pdb=" CBE Y01 A 603 " pdb=" CBG Y01 A 603 " both_signs ideal model delta sigma weight residual False 2.94 2.61 0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 916 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 544 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.84e+00 pdb=" C GLU A 544 " 0.029 2.00e-02 2.50e+03 pdb=" O GLU A 544 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 545 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 86 " 0.021 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO B 87 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 545 " -0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" C LEU A 545 " 0.020 2.00e-02 2.50e+03 pdb=" O LEU A 545 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE A 546 " -0.007 2.00e-02 2.50e+03 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 454 2.74 - 3.28: 5804 3.28 - 3.82: 10316 3.82 - 4.36: 11542 4.36 - 4.90: 20548 Nonbonded interactions: 48664 Sorted by model distance: nonbonded pdb=" OD2 ASP A 203 " pdb="MN MN A 605 " model vdw 2.204 2.320 nonbonded pdb=" OE2 GLU A 93 " pdb="MN MN A 604 " model vdw 2.247 2.320 nonbonded pdb=" O TRP A 234 " pdb=" OG1 THR A 539 " model vdw 2.269 2.440 nonbonded pdb=" OE1 GLN A 506 " pdb=" OG1 THR B 56 " model vdw 2.296 2.440 nonbonded pdb=" OD2 ASP B 104 " pdb=" OG1 THR B 107 " model vdw 2.321 2.440 ... (remaining 48659 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.50 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 3.820 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.730 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 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 : 0.008 0.230 6242 Z= 0.499 Angle : 0.770 16.370 8469 Z= 0.303 Chirality : 0.049 0.395 919 Planarity : 0.003 0.031 1040 Dihedral : 14.940 140.099 2342 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.16 % Allowed : 0.47 % Favored : 99.37 % 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: 2.53 (0.32), residues: 735 helix: 2.59 (0.30), residues: 316 sheet: 2.50 (0.42), residues: 161 loop : -0.08 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP A 346 HIS 0.001 0.000 HIS A 552 PHE 0.014 0.001 PHE A 49 TYR 0.008 0.001 TYR A 414 ARG 0.001 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.690 Fit side-chains REVERT: C 28 ILE cc_start: 0.7720 (mm) cc_final: 0.7186 (mm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.8553 time to fit residues: 128.2535 Evaluate side-chains 109 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.2980 chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 18 optimal weight: 0.0870 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 0.1980 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 0.0870 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 338 GLN A 537 ASN B 39 GLN B 73 ASN B 119 GLN C 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6242 Z= 0.119 Angle : 0.476 7.223 8469 Z= 0.243 Chirality : 0.039 0.133 919 Planarity : 0.003 0.024 1040 Dihedral : 9.483 109.286 1008 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.16 % Allowed : 9.95 % Favored : 86.89 % 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: 2.51 (0.31), residues: 735 helix: 2.77 (0.30), residues: 317 sheet: 2.09 (0.40), residues: 160 loop : -0.06 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.001 0.000 HIS A 360 PHE 0.013 0.001 PHE A 49 TYR 0.013 0.001 TYR A 550 ARG 0.002 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 0.729 Fit side-chains REVERT: A 239 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8306 (tp) REVERT: A 406 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8353 (mm) REVERT: C 85 LEU cc_start: 0.8898 (mp) cc_final: 0.8694 (mt) outliers start: 19 outliers final: 4 residues processed: 130 average time/residue: 0.8798 time to fit residues: 121.6848 Evaluate side-chains 123 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 79 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 0.0870 chunk 55 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 18 optimal weight: 0.0060 chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.7376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6242 Z= 0.182 Angle : 0.519 8.756 8469 Z= 0.271 Chirality : 0.041 0.139 919 Planarity : 0.003 0.033 1040 Dihedral : 9.149 90.733 1008 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.48 % Allowed : 12.16 % Favored : 84.36 % 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: 2.30 (0.31), residues: 735 helix: 2.56 (0.29), residues: 318 sheet: 2.07 (0.40), residues: 153 loop : -0.12 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.003 0.001 HIS A 360 PHE 0.015 0.002 PHE A 49 TYR 0.019 0.001 TYR A 414 ARG 0.005 0.000 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 0.732 Fit side-chains REVERT: A 348 ARG cc_start: 0.8022 (ttm110) cc_final: 0.7761 (ttm110) REVERT: C 25 SER cc_start: 0.9014 (m) cc_final: 0.8735 (p) outliers start: 21 outliers final: 10 residues processed: 126 average time/residue: 0.9308 time to fit residues: 124.3612 Evaluate side-chains 123 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 70 optimal weight: 0.9990 chunk 63 optimal weight: 0.0030 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6242 Z= 0.153 Angle : 0.496 8.542 8469 Z= 0.253 Chirality : 0.041 0.225 919 Planarity : 0.003 0.032 1040 Dihedral : 8.800 80.768 1008 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 3.48 % Allowed : 14.38 % Favored : 82.15 % 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: 2.24 (0.31), residues: 735 helix: 2.53 (0.29), residues: 320 sheet: 2.04 (0.40), residues: 151 loop : -0.19 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 472 HIS 0.002 0.001 HIS A 360 PHE 0.014 0.001 PHE A 49 TYR 0.017 0.001 TYR C 106 ARG 0.007 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 0.701 Fit side-chains REVERT: A 239 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8287 (tp) REVERT: B 38 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7865 (mtp180) REVERT: C 25 SER cc_start: 0.8976 (m) cc_final: 0.8718 (p) outliers start: 21 outliers final: 7 residues processed: 117 average time/residue: 1.0037 time to fit residues: 124.0149 Evaluate side-chains 111 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 63 optimal weight: 0.0170 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN B 73 ASN C 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 6242 Z= 0.351 Angle : 0.610 5.546 8469 Z= 0.326 Chirality : 0.046 0.158 919 Planarity : 0.004 0.039 1040 Dihedral : 9.687 69.055 1008 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.78 % Favored : 98.09 % Rotamer: Outliers : 5.21 % Allowed : 14.06 % Favored : 80.73 % 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: 1.72 (0.30), residues: 735 helix: 2.12 (0.28), residues: 319 sheet: 1.60 (0.39), residues: 164 loop : -0.48 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 472 HIS 0.006 0.002 HIS A 360 PHE 0.017 0.002 PHE A 49 TYR 0.019 0.002 TYR A 414 ARG 0.004 0.001 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 104 time to evaluate : 0.685 Fit side-chains REVERT: B 18 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8464 (mm) REVERT: B 38 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7875 (mtp180) REVERT: C 118 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7298 (mm-40) outliers start: 32 outliers final: 12 residues processed: 122 average time/residue: 1.0246 time to fit residues: 131.8236 Evaluate side-chains 112 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 120 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 68 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN B 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6242 Z= 0.158 Angle : 0.511 8.724 8469 Z= 0.265 Chirality : 0.042 0.218 919 Planarity : 0.003 0.037 1040 Dihedral : 9.237 65.130 1008 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.53 % Allowed : 17.22 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.30), residues: 735 helix: 2.30 (0.29), residues: 319 sheet: 1.73 (0.38), residues: 161 loop : -0.40 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 472 HIS 0.003 0.001 HIS A 360 PHE 0.017 0.001 PHE A 49 TYR 0.019 0.001 TYR C 106 ARG 0.003 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.622 Fit side-chains REVERT: B 18 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8435 (mm) REVERT: B 38 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7834 (mtp180) REVERT: C 25 SER cc_start: 0.9051 (m) cc_final: 0.8765 (p) outliers start: 15 outliers final: 10 residues processed: 111 average time/residue: 1.0148 time to fit residues: 118.9372 Evaluate side-chains 110 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 0.0050 chunk 51 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 0.0070 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 overall best weight: 0.4812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6242 Z= 0.157 Angle : 0.516 8.954 8469 Z= 0.266 Chirality : 0.042 0.302 919 Planarity : 0.003 0.038 1040 Dihedral : 9.048 64.259 1008 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.21 % Allowed : 19.12 % Favored : 78.67 % 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: 1.94 (0.30), residues: 735 helix: 2.38 (0.29), residues: 317 sheet: 1.68 (0.38), residues: 161 loop : -0.40 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 472 HIS 0.002 0.001 HIS A 360 PHE 0.015 0.001 PHE A 49 TYR 0.019 0.001 TYR C 106 ARG 0.003 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 0.707 Fit side-chains REVERT: A 247 ARG cc_start: 0.8250 (tpp-160) cc_final: 0.7953 (tpm-80) REVERT: B 18 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8438 (mm) REVERT: B 38 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7825 (mtp180) REVERT: C 25 SER cc_start: 0.9040 (m) cc_final: 0.8763 (p) REVERT: C 89 ASP cc_start: 0.7996 (m-30) cc_final: 0.7633 (m-30) outliers start: 13 outliers final: 8 residues processed: 111 average time/residue: 1.0635 time to fit residues: 124.5370 Evaluate side-chains 108 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6242 Z= 0.185 Angle : 0.530 7.772 8469 Z= 0.274 Chirality : 0.043 0.296 919 Planarity : 0.003 0.040 1040 Dihedral : 9.003 62.571 1008 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.37 % Allowed : 18.96 % Favored : 78.67 % 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: 1.90 (0.30), residues: 735 helix: 2.35 (0.29), residues: 317 sheet: 1.70 (0.38), residues: 161 loop : -0.46 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 472 HIS 0.003 0.001 HIS A 360 PHE 0.015 0.001 PHE A 49 TYR 0.019 0.001 TYR C 106 ARG 0.003 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.703 Fit side-chains REVERT: B 3 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7625 (mp-120) REVERT: B 18 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8465 (mm) REVERT: B 38 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7896 (mtp180) REVERT: C 25 SER cc_start: 0.9036 (m) cc_final: 0.8762 (p) outliers start: 14 outliers final: 11 residues processed: 110 average time/residue: 1.0313 time to fit residues: 119.7840 Evaluate side-chains 111 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 0.0970 chunk 43 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6242 Z= 0.183 Angle : 0.525 8.011 8469 Z= 0.273 Chirality : 0.043 0.285 919 Planarity : 0.003 0.040 1040 Dihedral : 8.776 60.742 1008 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.69 % Allowed : 18.33 % Favored : 78.99 % 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: 1.89 (0.30), residues: 735 helix: 2.34 (0.29), residues: 317 sheet: 1.67 (0.38), residues: 161 loop : -0.43 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 472 HIS 0.003 0.001 HIS A 360 PHE 0.015 0.001 PHE A 49 TYR 0.021 0.001 TYR C 106 ARG 0.003 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.789 Fit side-chains REVERT: B 18 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8478 (mm) REVERT: B 38 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7896 (mtp180) REVERT: C 25 SER cc_start: 0.9006 (m) cc_final: 0.8757 (p) outliers start: 16 outliers final: 11 residues processed: 111 average time/residue: 1.0094 time to fit residues: 118.4350 Evaluate side-chains 111 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.0970 chunk 46 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 17 optimal weight: 0.0870 overall best weight: 0.4960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN B 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6242 Z= 0.153 Angle : 0.517 8.187 8469 Z= 0.267 Chirality : 0.042 0.273 919 Planarity : 0.003 0.039 1040 Dihedral : 8.503 59.200 1008 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.53 % Allowed : 18.64 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.30), residues: 735 helix: 2.38 (0.29), residues: 317 sheet: 1.69 (0.38), residues: 161 loop : -0.41 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 472 HIS 0.002 0.001 HIS A 360 PHE 0.015 0.001 PHE A 49 TYR 0.021 0.001 TYR C 106 ARG 0.003 0.000 ARG B 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.766 Fit side-chains REVERT: B 18 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8478 (mm) REVERT: B 38 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7880 (mtp180) REVERT: C 25 SER cc_start: 0.8960 (m) cc_final: 0.8745 (p) outliers start: 15 outliers final: 11 residues processed: 110 average time/residue: 1.0359 time to fit residues: 120.4594 Evaluate side-chains 110 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3251 r_free = 0.3251 target = 0.084339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.067848 restraints weight = 24544.461| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.86 r_work: 0.2785 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6242 Z= 0.229 Angle : 0.560 8.165 8469 Z= 0.291 Chirality : 0.044 0.276 919 Planarity : 0.003 0.041 1040 Dihedral : 8.500 57.832 1008 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.37 % Allowed : 18.80 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.30), residues: 735 helix: 2.30 (0.29), residues: 317 sheet: 1.52 (0.38), residues: 163 loop : -0.41 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 472 HIS 0.003 0.001 HIS A 360 PHE 0.015 0.001 PHE A 49 TYR 0.021 0.002 TYR C 106 ARG 0.004 0.000 ARG C 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2734.12 seconds wall clock time: 49 minutes 12.75 seconds (2952.75 seconds total)