Starting phenix.real_space_refine on Thu Sep 18 13:59:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nv3_49827/09_2025/9nv3_49827.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nv3_49827/09_2025/9nv3_49827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nv3_49827/09_2025/9nv3_49827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nv3_49827/09_2025/9nv3_49827.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nv3_49827/09_2025/9nv3_49827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nv3_49827/09_2025/9nv3_49827.map" } resolution = 4.45 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.056 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 S 30 5.16 5 C 5523 2.51 5 N 1511 2.21 5 O 1620 1.98 5 H 8603 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17287 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3229 Classifications: {'peptide': 199} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "C" Number of atoms: 14058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 866, 14058 Classifications: {'peptide': 866} Link IDs: {'PTRANS': 29, 'TRANS': 836} Time building chain proxies: 2.97, per 1000 atoms: 0.17 Number of scatterers: 17287 At special positions: 0 Unit cell: (86.394, 117.81, 159.324, 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) S 30 16.00 O 1620 8.00 N 1511 7.00 C 5523 6.00 H 8603 1.00 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: 1.04 Conformation dependent library (CDL) restraints added in 466.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 49.6% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 4 through 20 removed outlier: 4.053A pdb=" N GLN A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 26 Processing helix chain 'A' and resid 44 through 59 removed outlier: 3.880A pdb=" N ARG A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 70 through 76 removed outlier: 3.965A pdb=" N ILE A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.641A pdb=" N VAL A 94 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 removed outlier: 3.882A pdb=" N LEU A 99 " --> pdb=" O GLY A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 111 removed outlier: 3.851A pdb=" N LYS A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 108 through 111' Processing helix chain 'A' and resid 112 through 120 removed outlier: 4.602A pdb=" N ILE A 116 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'C' and resid 3 through 17 Processing helix chain 'C' and resid 52 through 62 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 114 through 121 Processing helix chain 'C' and resid 122 through 125 removed outlier: 3.799A pdb=" N PHE C 125 " --> pdb=" O LYS C 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 125' Processing helix chain 'C' and resid 126 through 135 Processing helix chain 'C' and resid 142 through 156 Processing helix chain 'C' and resid 161 through 177 Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 195 through 207 removed outlier: 3.568A pdb=" N VAL C 199 " --> pdb=" O ASP C 195 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN C 205 " --> pdb=" O TRP C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 232 removed outlier: 3.536A pdb=" N ASP C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 242 Processing helix chain 'C' and resid 248 through 265 Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 271 through 279 removed outlier: 3.966A pdb=" N ALA C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLN C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 290 Processing helix chain 'C' and resid 294 through 300 removed outlier: 3.599A pdb=" N HIS C 298 " --> pdb=" O TYR C 295 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU C 299 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 320 Processing helix chain 'C' and resid 326 through 333 removed outlier: 3.831A pdb=" N LEU C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 340 Processing helix chain 'C' and resid 340 through 346 Processing helix chain 'C' and resid 346 through 369 removed outlier: 3.540A pdb=" N CYS C 350 " --> pdb=" O ARG C 346 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR C 353 " --> pdb=" O TYR C 349 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP C 354 " --> pdb=" O CYS C 350 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 388 Processing helix chain 'C' and resid 390 through 407 removed outlier: 3.799A pdb=" N TYR C 396 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 416 through 428 Processing helix chain 'C' and resid 428 through 445 removed outlier: 4.024A pdb=" N LEU C 433 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C 434 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG C 435 " --> pdb=" O ALA C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 449 Processing helix chain 'C' and resid 460 through 465 Processing helix chain 'C' and resid 466 through 472 removed outlier: 3.737A pdb=" N ASN C 471 " --> pdb=" O PRO C 468 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN C 472 " --> pdb=" O GLN C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 497 removed outlier: 5.561A pdb=" N GLY C 495 " --> pdb=" O ALA C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 525 removed outlier: 3.656A pdb=" N GLY C 522 " --> pdb=" O TYR C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 558 Processing helix chain 'C' and resid 559 through 563 Processing helix chain 'C' and resid 571 through 575 removed outlier: 4.287A pdb=" N LYS C 574 " --> pdb=" O ASP C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 582 Processing helix chain 'C' and resid 597 through 602 removed outlier: 3.527A pdb=" N ASP C 602 " --> pdb=" O ASP C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 607 Processing helix chain 'C' and resid 609 through 622 removed outlier: 4.772A pdb=" N VAL C 618 " --> pdb=" O CYS C 614 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS C 622 " --> pdb=" O VAL C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 695 Processing helix chain 'C' and resid 726 through 730 Processing helix chain 'C' and resid 815 through 819 removed outlier: 4.226A pdb=" N ARG C 819 " --> pdb=" O MET C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 866 Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 181 removed outlier: 4.755A pdb=" N ARG A 180 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 69 removed outlier: 6.480A pdb=" N ALA A 66 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N THR A 131 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU A 68 " --> pdb=" O THR A 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 44 through 47 removed outlier: 6.529A pdb=" N THR C 44 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N TRP C 72 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU C 46 " --> pdb=" O TRP C 72 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE C 73 " --> pdb=" O TRP C 24 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR C 93 " --> pdb=" O ILE C 21 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 479 through 483 removed outlier: 6.736A pdb=" N MET C 565 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N TRP C 593 " --> pdb=" O MET C 565 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL C 567 " --> pdb=" O TRP C 593 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 506 through 507 Processing sheet with id=AA6, first strand: chain 'C' and resid 511 through 512 Processing sheet with id=AA7, first strand: chain 'C' and resid 532 through 533 Processing sheet with id=AA8, first strand: chain 'C' and resid 670 through 671 Processing sheet with id=AA9, first strand: chain 'C' and resid 769 through 772 Processing sheet with id=AB1, first strand: chain 'C' and resid 800 through 807 removed outlier: 7.852A pdb=" N VAL C 801 " --> pdb=" O ASP C 795 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ASP C 795 " --> pdb=" O VAL C 801 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLY C 803 " --> pdb=" O ILE C 793 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE C 793 " --> pdb=" O GLY C 803 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR C 838 " --> pdb=" O VAL C 856 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 897 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: 3.92 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.35: 11480 1.35 - 1.75: 5942 1.75 - 2.15: 49 2.15 - 2.56: 0 2.56 - 2.96: 1 Bond restraints: 17472 Sorted by residual: bond pdb=" CG GLU C 321 " pdb=" CD GLU C 321 " ideal model delta sigma weight residual 1.516 2.961 -1.445 2.50e-02 1.60e+03 3.34e+03 bond pdb=" CG TYR C 420 " pdb=" CD2 TYR C 420 " ideal model delta sigma weight residual 1.389 1.747 -0.358 2.10e-02 2.27e+03 2.91e+02 bond pdb=" CG TYR C 420 " pdb=" CD1 TYR C 420 " ideal model delta sigma weight residual 1.389 1.739 -0.350 2.10e-02 2.27e+03 2.78e+02 bond pdb=" CE1 TYR C 420 " pdb=" CZ TYR C 420 " ideal model delta sigma weight residual 1.378 1.747 -0.369 2.40e-02 1.74e+03 2.36e+02 bond pdb=" CE2 TYR C 420 " pdb=" CZ TYR C 420 " ideal model delta sigma weight residual 1.378 1.742 -0.364 2.40e-02 1.74e+03 2.30e+02 ... (remaining 17467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.67: 31337 7.67 - 15.34: 210 15.34 - 23.01: 4 23.01 - 30.68: 3 30.68 - 38.35: 8 Bond angle restraints: 31562 Sorted by residual: angle pdb=" C GLU A 80 " pdb=" CA GLU A 80 " pdb=" HA GLU A 80 " ideal model delta sigma weight residual 109.00 70.65 38.35 3.00e+00 1.11e-01 1.63e+02 angle pdb=" N LYS C 738 " pdb=" CA LYS C 738 " pdb=" HA LYS C 738 " ideal model delta sigma weight residual 110.00 72.39 37.61 3.00e+00 1.11e-01 1.57e+02 angle pdb=" CB GLU A 80 " pdb=" CA GLU A 80 " pdb=" HA GLU A 80 " ideal model delta sigma weight residual 109.00 75.35 33.65 3.00e+00 1.11e-01 1.26e+02 angle pdb=" N LEU A 106 " pdb=" CA LEU A 106 " pdb=" HA LEU A 106 " ideal model delta sigma weight residual 110.00 76.52 33.48 3.00e+00 1.11e-01 1.25e+02 angle pdb=" N LEU A 106 " pdb=" CA LEU A 106 " pdb=" C LEU A 106 " ideal model delta sigma weight residual 110.53 125.12 -14.59 1.32e+00 5.74e-01 1.22e+02 ... (remaining 31557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7151 17.95 - 35.90: 715 35.90 - 53.85: 172 53.85 - 71.80: 106 71.80 - 89.76: 23 Dihedral angle restraints: 8167 sinusoidal: 4453 harmonic: 3714 Sorted by residual: dihedral pdb=" C TYR C 784 " pdb=" N TYR C 784 " pdb=" CA TYR C 784 " pdb=" CB TYR C 784 " ideal model delta harmonic sigma weight residual -122.60 -141.81 19.21 0 2.50e+00 1.60e-01 5.91e+01 dihedral pdb=" C TRP A 137 " pdb=" N TRP A 137 " pdb=" CA TRP A 137 " pdb=" CB TRP A 137 " ideal model delta harmonic sigma weight residual -122.60 -140.81 18.21 0 2.50e+00 1.60e-01 5.30e+01 dihedral pdb=" C GLU A 80 " pdb=" N GLU A 80 " pdb=" CA GLU A 80 " pdb=" CB GLU A 80 " ideal model delta harmonic sigma weight residual -122.60 -140.19 17.59 0 2.50e+00 1.60e-01 4.95e+01 ... (remaining 8164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 1112 0.151 - 0.302: 180 0.302 - 0.453: 16 0.453 - 0.604: 2 0.604 - 0.755: 4 Chirality restraints: 1314 Sorted by residual: chirality pdb=" CA TRP A 137 " pdb=" N TRP A 137 " pdb=" C TRP A 137 " pdb=" CB TRP A 137 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CA TYR C 784 " pdb=" N TYR C 784 " pdb=" C TYR C 784 " pdb=" CB TYR C 784 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" CA LEU A 106 " pdb=" N LEU A 106 " pdb=" C LEU A 106 " pdb=" CB LEU A 106 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 ... (remaining 1311 not shown) Planarity restraints: 2589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 262 " -0.444 2.00e-02 2.50e+03 1.74e-01 1.20e+03 pdb=" CG TRP C 262 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP C 262 " 0.068 2.00e-02 2.50e+03 pdb=" CD2 TRP C 262 " 0.108 2.00e-02 2.50e+03 pdb=" NE1 TRP C 262 " 0.220 2.00e-02 2.50e+03 pdb=" CE2 TRP C 262 " 0.070 2.00e-02 2.50e+03 pdb=" CE3 TRP C 262 " 0.135 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 262 " -0.112 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 262 " 0.078 2.00e-02 2.50e+03 pdb=" CH2 TRP C 262 " -0.080 2.00e-02 2.50e+03 pdb=" HD1 TRP C 262 " -0.083 2.00e-02 2.50e+03 pdb=" HE1 TRP C 262 " 0.214 2.00e-02 2.50e+03 pdb=" HE3 TRP C 262 " 0.163 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 262 " -0.228 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 262 " 0.091 2.00e-02 2.50e+03 pdb=" HH2 TRP C 262 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 428 " -0.445 2.00e-02 2.50e+03 1.66e-01 1.11e+03 pdb=" CG TRP C 428 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP C 428 " 0.078 2.00e-02 2.50e+03 pdb=" CD2 TRP C 428 " 0.098 2.00e-02 2.50e+03 pdb=" NE1 TRP C 428 " 0.133 2.00e-02 2.50e+03 pdb=" CE2 TRP C 428 " 0.037 2.00e-02 2.50e+03 pdb=" CE3 TRP C 428 " 0.130 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 428 " -0.091 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 428 " 0.078 2.00e-02 2.50e+03 pdb=" CH2 TRP C 428 " -0.075 2.00e-02 2.50e+03 pdb=" HD1 TRP C 428 " -0.056 2.00e-02 2.50e+03 pdb=" HE1 TRP C 428 " 0.248 2.00e-02 2.50e+03 pdb=" HE3 TRP C 428 " 0.143 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 428 " -0.218 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 428 " 0.101 2.00e-02 2.50e+03 pdb=" HH2 TRP C 428 " -0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 687 " 0.434 2.00e-02 2.50e+03 1.61e-01 1.04e+03 pdb=" CG TRP C 687 " 0.088 2.00e-02 2.50e+03 pdb=" CD1 TRP C 687 " -0.077 2.00e-02 2.50e+03 pdb=" CD2 TRP C 687 " -0.076 2.00e-02 2.50e+03 pdb=" NE1 TRP C 687 " -0.131 2.00e-02 2.50e+03 pdb=" CE2 TRP C 687 " -0.057 2.00e-02 2.50e+03 pdb=" CE3 TRP C 687 " -0.119 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 687 " 0.073 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 687 " -0.105 2.00e-02 2.50e+03 pdb=" CH2 TRP C 687 " 0.041 2.00e-02 2.50e+03 pdb=" HD1 TRP C 687 " -0.073 2.00e-02 2.50e+03 pdb=" HE1 TRP C 687 " -0.165 2.00e-02 2.50e+03 pdb=" HE3 TRP C 687 " -0.119 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 687 " 0.250 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 687 " -0.133 2.00e-02 2.50e+03 pdb=" HH2 TRP C 687 " 0.169 2.00e-02 2.50e+03 ... (remaining 2586 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 1235 2.14 - 2.75: 30492 2.75 - 3.37: 55296 3.37 - 3.98: 71253 3.98 - 4.60: 103501 Nonbonded interactions: 261777 Sorted by model distance: nonbonded pdb=" H ALA C 641 " pdb=" HD2 PRO C 733 " model vdw 1.519 2.270 nonbonded pdb=" OD2 ASP C 234 " pdb=" HG SER C 292 " model vdw 1.562 2.450 nonbonded pdb=" H VAL C 754 " pdb=" HB3 TYR C 784 " model vdw 1.572 2.270 nonbonded pdb=" HG1 THR C 519 " pdb=" OD2 ASP C 642 " model vdw 1.602 2.450 nonbonded pdb=" HG1 THR C 162 " pdb=" OE1 GLU C 207 " model vdw 1.603 2.450 ... (remaining 261772 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.050 Find NCS groups from input model: 0.040 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5403 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 : 0.022 1.445 8869 Z= 1.112 Angle : 2.141 21.856 12004 Z= 1.403 Chirality : 0.118 0.755 1314 Planarity : 0.021 0.206 1564 Dihedral : 16.920 89.755 3330 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 3.20 % Allowed : 14.04 % Favored : 82.75 % Rotamer: Outliers : 3.51 % Allowed : 7.65 % Favored : 88.84 % Cbeta Deviations : 1.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.24 (0.23), residues: 1061 helix: -3.23 (0.18), residues: 419 sheet: -1.69 (0.78), residues: 45 loop : -2.63 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG C 446 TYR 0.237 0.032 TYR C 353 PHE 0.190 0.021 PHE C 399 TRP 0.309 0.051 TRP C 428 HIS 0.027 0.006 HIS C 369 Details of bonding type rmsd covalent geometry : bond 0.02247 ( 8869) covalent geometry : angle 2.14149 (12004) hydrogen bonds : bond 0.15898 ( 330) hydrogen bonds : angle 9.63694 ( 897) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ILE cc_start: 0.8176 (mt) cc_final: 0.7879 (mm) REVERT: C 174 VAL cc_start: 0.7641 (t) cc_final: 0.7403 (p) REVERT: C 290 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.6739 (tpm170) REVERT: C 568 LYS cc_start: 0.6658 (mttt) cc_final: 0.5733 (mmpt) outliers start: 33 outliers final: 24 residues processed: 151 average time/residue: 0.2716 time to fit residues: 53.3733 Evaluate side-chains 118 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.088250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.063090 restraints weight = 185811.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.066988 restraints weight = 113221.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.069319 restraints weight = 78938.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.070938 restraints weight = 60521.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.072003 restraints weight = 50191.070| |-----------------------------------------------------------------------------| r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.110 8869 Z= 0.690 Angle : 1.065 17.751 12004 Z= 0.584 Chirality : 0.055 0.448 1314 Planarity : 0.008 0.126 1564 Dihedral : 10.767 42.461 1165 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.94 % Allowed : 13.76 % Favored : 85.30 % Rotamer: Outliers : 0.11 % Allowed : 3.61 % Favored : 96.28 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 1.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.93 (0.23), residues: 1061 helix: -2.32 (0.21), residues: 429 sheet: -2.50 (0.56), residues: 70 loop : -2.90 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 184 TYR 0.044 0.003 TYR C 784 PHE 0.028 0.003 PHE C 258 TRP 0.031 0.003 TRP C 262 HIS 0.009 0.003 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.01735 ( 8869) covalent geometry : angle 1.06509 (12004) hydrogen bonds : bond 0.06446 ( 330) hydrogen bonds : angle 7.86365 ( 897) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 MET cc_start: 0.9437 (mtt) cc_final: 0.9120 (mtt) REVERT: C 268 TYR cc_start: 0.7179 (m-80) cc_final: 0.6611 (m-80) REVERT: C 429 TYR cc_start: 0.8181 (t80) cc_final: 0.7967 (t80) REVERT: C 523 MET cc_start: 0.6287 (mtt) cc_final: 0.6021 (mtt) REVERT: C 526 LEU cc_start: 0.8885 (mt) cc_final: 0.8671 (mt) REVERT: C 567 VAL cc_start: 0.9219 (p) cc_final: 0.8997 (p) REVERT: C 568 LYS cc_start: 0.7883 (mttt) cc_final: 0.7621 (mmpt) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.2411 time to fit residues: 34.0927 Evaluate side-chains 85 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 10 optimal weight: 0.0970 chunk 81 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN C 67 GLN C 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.090526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.066357 restraints weight = 208519.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.070334 restraints weight = 124497.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.072679 restraints weight = 84353.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.074230 restraints weight = 65175.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.074771 restraints weight = 53991.895| |-----------------------------------------------------------------------------| r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.121 8869 Z= 0.676 Angle : 0.943 18.102 12004 Z= 0.508 Chirality : 0.052 0.417 1314 Planarity : 0.007 0.072 1564 Dihedral : 10.116 40.178 1165 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.57 % Allowed : 13.57 % Favored : 85.86 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.78 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.88 (0.23), residues: 1061 helix: -2.20 (0.21), residues: 432 sheet: -2.37 (0.50), residues: 83 loop : -2.97 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 366 TYR 0.031 0.003 TYR C 353 PHE 0.024 0.003 PHE C 8 TRP 0.023 0.003 TRP C 262 HIS 0.013 0.002 HIS C 369 Details of bonding type rmsd covalent geometry : bond 0.01717 ( 8869) covalent geometry : angle 0.94282 (12004) hydrogen bonds : bond 0.05551 ( 330) hydrogen bonds : angle 7.52856 ( 897) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.3742 (mmm) cc_final: 0.3540 (mmm) REVERT: C 164 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8743 (mp0) REVERT: C 226 CYS cc_start: 0.9034 (m) cc_final: 0.8430 (t) REVERT: C 269 LYS cc_start: 0.9295 (tmmt) cc_final: 0.9061 (pttm) REVERT: C 429 TYR cc_start: 0.8002 (t80) cc_final: 0.7755 (t80) REVERT: C 523 MET cc_start: 0.6331 (mtt) cc_final: 0.6036 (mtt) REVERT: C 568 LYS cc_start: 0.7961 (mttt) cc_final: 0.7534 (mmpt) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2527 time to fit residues: 34.3908 Evaluate side-chains 84 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 93 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 14 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4537 r_free = 0.4537 target = 0.089980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.064530 restraints weight = 207766.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.068552 restraints weight = 126594.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.070850 restraints weight = 86540.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.071651 restraints weight = 67655.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.073006 restraints weight = 58830.889| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.120 8869 Z= 0.670 Angle : 0.876 17.989 12004 Z= 0.471 Chirality : 0.050 0.404 1314 Planarity : 0.006 0.064 1564 Dihedral : 9.631 38.527 1165 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.57 % Allowed : 13.20 % Favored : 86.24 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.65 (0.23), residues: 1061 helix: -1.91 (0.22), residues: 427 sheet: -2.39 (0.51), residues: 83 loop : -2.90 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 631 TYR 0.031 0.002 TYR C 420 PHE 0.023 0.002 PHE C 258 TRP 0.018 0.003 TRP C 428 HIS 0.020 0.002 HIS C 407 Details of bonding type rmsd covalent geometry : bond 0.01705 ( 8869) covalent geometry : angle 0.87610 (12004) hydrogen bonds : bond 0.05105 ( 330) hydrogen bonds : angle 7.19135 ( 897) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 MET cc_start: 0.7980 (mmp) cc_final: 0.7700 (mmm) REVERT: C 213 GLU cc_start: 0.8801 (mp0) cc_final: 0.8270 (tp30) REVERT: C 226 CYS cc_start: 0.9026 (m) cc_final: 0.8408 (t) REVERT: C 429 TYR cc_start: 0.8028 (t80) cc_final: 0.7731 (t80) REVERT: C 526 LEU cc_start: 0.8974 (mt) cc_final: 0.8724 (mt) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2531 time to fit residues: 32.7097 Evaluate side-chains 77 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 16 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4546 r_free = 0.4546 target = 0.092181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.067965 restraints weight = 193261.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.071930 restraints weight = 117978.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.074104 restraints weight = 81175.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.075622 restraints weight = 63655.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.076463 restraints weight = 53563.107| |-----------------------------------------------------------------------------| r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.120 8869 Z= 0.666 Angle : 0.843 18.041 12004 Z= 0.451 Chirality : 0.050 0.417 1314 Planarity : 0.006 0.066 1564 Dihedral : 9.284 38.899 1165 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.38 % Allowed : 13.38 % Favored : 86.24 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.59 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.46 (0.24), residues: 1061 helix: -1.62 (0.23), residues: 431 sheet: -2.13 (0.54), residues: 79 loop : -2.95 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 819 TYR 0.032 0.003 TYR C 420 PHE 0.024 0.002 PHE C 23 TRP 0.036 0.003 TRP C 575 HIS 0.015 0.002 HIS C 407 Details of bonding type rmsd covalent geometry : bond 0.01699 ( 8869) covalent geometry : angle 0.84270 (12004) hydrogen bonds : bond 0.04714 ( 330) hydrogen bonds : angle 6.89619 ( 897) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 GLU cc_start: 0.8869 (mp0) cc_final: 0.8349 (tm-30) REVERT: C 226 CYS cc_start: 0.8985 (m) cc_final: 0.8372 (t) REVERT: C 429 TYR cc_start: 0.8061 (t80) cc_final: 0.7758 (t80) REVERT: C 526 LEU cc_start: 0.8934 (mt) cc_final: 0.8694 (mt) REVERT: C 571 ASP cc_start: 0.8896 (t70) cc_final: 0.8444 (m-30) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2279 time to fit residues: 28.9721 Evaluate side-chains 84 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 57 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN C 317 GLN C 344 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.083967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.058587 restraints weight = 201717.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.062139 restraints weight = 122561.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.064266 restraints weight = 86437.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.065348 restraints weight = 67917.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.066382 restraints weight = 59348.595| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 1.111 8869 Z= 0.703 Angle : 0.924 17.796 12004 Z= 0.501 Chirality : 0.051 0.412 1314 Planarity : 0.007 0.083 1564 Dihedral : 9.404 35.711 1165 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 33.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 15.93 % Favored : 83.79 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.68 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.68 (0.24), residues: 1061 helix: -1.79 (0.23), residues: 419 sheet: -3.00 (0.52), residues: 78 loop : -2.94 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 477 TYR 0.036 0.003 TYR C 353 PHE 0.034 0.003 PHE C 399 TRP 0.024 0.003 TRP C 342 HIS 0.012 0.002 HIS C 407 Details of bonding type rmsd covalent geometry : bond 0.01755 ( 8869) covalent geometry : angle 0.92411 (12004) hydrogen bonds : bond 0.05620 ( 330) hydrogen bonds : angle 7.27301 ( 897) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 GLU cc_start: 0.8942 (mp0) cc_final: 0.8265 (tm-30) REVERT: C 354 ASP cc_start: 0.9590 (m-30) cc_final: 0.9260 (m-30) REVERT: C 412 MET cc_start: 0.8644 (tpp) cc_final: 0.8416 (tpp) REVERT: C 526 LEU cc_start: 0.8958 (mt) cc_final: 0.8721 (mt) REVERT: C 571 ASP cc_start: 0.8628 (t70) cc_final: 0.8328 (m-30) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2270 time to fit residues: 27.7849 Evaluate side-chains 80 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 661 GLN ** C 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.088983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.063555 restraints weight = 194143.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.067522 restraints weight = 118295.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.070051 restraints weight = 80339.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.071656 restraints weight = 61238.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.072682 restraints weight = 50600.681| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.118 8869 Z= 0.666 Angle : 0.834 18.005 12004 Z= 0.446 Chirality : 0.050 0.407 1314 Planarity : 0.007 0.090 1564 Dihedral : 9.167 37.989 1165 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.38 % Allowed : 13.76 % Favored : 85.86 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.46 (0.24), residues: 1061 helix: -1.58 (0.24), residues: 424 sheet: -3.03 (0.57), residues: 61 loop : -2.86 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 581 TYR 0.036 0.003 TYR C 420 PHE 0.021 0.002 PHE C 504 TRP 0.018 0.002 TRP C 262 HIS 0.013 0.002 HIS C 778 Details of bonding type rmsd covalent geometry : bond 0.01701 ( 8869) covalent geometry : angle 0.83375 (12004) hydrogen bonds : bond 0.04610 ( 330) hydrogen bonds : angle 6.91962 ( 897) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 GLU cc_start: 0.8918 (mp0) cc_final: 0.8280 (tm-30) REVERT: C 226 CYS cc_start: 0.9006 (m) cc_final: 0.8590 (t) REVERT: C 429 TYR cc_start: 0.8034 (t80) cc_final: 0.7480 (t80) REVERT: C 526 LEU cc_start: 0.9008 (mt) cc_final: 0.8795 (mt) REVERT: C 568 LYS cc_start: 0.8015 (mttt) cc_final: 0.7180 (mmpt) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2505 time to fit residues: 31.3899 Evaluate side-chains 83 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 104 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 427 ASN ** C 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.089511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.065766 restraints weight = 199540.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.069310 restraints weight = 119283.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.071598 restraints weight = 82974.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.072696 restraints weight = 63348.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.073812 restraints weight = 54821.741| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.106 8869 Z= 0.669 Angle : 0.823 16.798 12004 Z= 0.441 Chirality : 0.049 0.477 1314 Planarity : 0.007 0.135 1564 Dihedral : 8.982 38.268 1165 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 23.26 Ramachandran Plot: Outliers : 0.28 % Allowed : 15.27 % Favored : 84.45 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.59 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.31 (0.24), residues: 1061 helix: -1.46 (0.24), residues: 423 sheet: -2.64 (0.57), residues: 68 loop : -2.81 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 581 TYR 0.028 0.002 TYR C 353 PHE 0.025 0.002 PHE C 504 TRP 0.017 0.002 TRP C 687 HIS 0.012 0.002 HIS C 25 Details of bonding type rmsd covalent geometry : bond 0.01713 ( 8869) covalent geometry : angle 0.82315 (12004) hydrogen bonds : bond 0.04659 ( 330) hydrogen bonds : angle 6.84628 ( 897) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.3279 (mmm) cc_final: 0.3064 (mmm) REVERT: C 213 GLU cc_start: 0.8884 (mp0) cc_final: 0.8235 (tm-30) REVERT: C 414 LEU cc_start: 0.8061 (mt) cc_final: 0.7669 (mt) REVERT: C 429 TYR cc_start: 0.8180 (t80) cc_final: 0.7619 (t80) REVERT: C 526 LEU cc_start: 0.8965 (mt) cc_final: 0.8748 (mt) REVERT: C 568 LYS cc_start: 0.7761 (mttt) cc_final: 0.7138 (mmpt) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2424 time to fit residues: 30.0784 Evaluate side-chains 81 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 38 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN C 278 GLN ** C 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.092108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.072365 restraints weight = 245992.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.075440 restraints weight = 147933.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.077525 restraints weight = 102014.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.078425 restraints weight = 77493.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.079580 restraints weight = 66740.587| |-----------------------------------------------------------------------------| r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.103 8869 Z= 0.677 Angle : 0.845 16.954 12004 Z= 0.454 Chirality : 0.050 0.451 1314 Planarity : 0.008 0.159 1564 Dihedral : 8.939 37.662 1165 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 26.50 Ramachandran Plot: Outliers : 0.28 % Allowed : 15.27 % Favored : 84.45 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.39 (0.24), residues: 1061 helix: -1.45 (0.24), residues: 419 sheet: -2.68 (0.56), residues: 68 loop : -2.91 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 581 TYR 0.037 0.003 TYR C 462 PHE 0.038 0.002 PHE C 381 TRP 0.030 0.003 TRP C 428 HIS 0.013 0.002 HIS C 96 Details of bonding type rmsd covalent geometry : bond 0.01729 ( 8869) covalent geometry : angle 0.84461 (12004) hydrogen bonds : bond 0.04821 ( 330) hydrogen bonds : angle 6.87494 ( 897) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.3479 (mmm) cc_final: 0.3239 (mmm) REVERT: C 213 GLU cc_start: 0.8937 (mp0) cc_final: 0.8258 (tm-30) REVERT: C 414 LEU cc_start: 0.8068 (mt) cc_final: 0.7670 (mt) REVERT: C 523 MET cc_start: 0.5787 (mtt) cc_final: 0.5508 (mtt) REVERT: C 526 LEU cc_start: 0.8857 (mt) cc_final: 0.8631 (mt) REVERT: C 726 MET cc_start: 0.9233 (mmm) cc_final: 0.8786 (mmm) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2481 time to fit residues: 31.0047 Evaluate side-chains 83 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 100 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 96 HIS ** C 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.086610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.061162 restraints weight = 196133.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.065115 restraints weight = 119463.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.067516 restraints weight = 82091.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.069134 restraints weight = 63611.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.070171 restraints weight = 52622.480| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.104 8869 Z= 0.680 Angle : 0.849 16.870 12004 Z= 0.458 Chirality : 0.050 0.443 1314 Planarity : 0.008 0.167 1564 Dihedral : 8.931 37.162 1165 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 27.08 Ramachandran Plot: Outliers : 0.38 % Allowed : 15.93 % Favored : 83.69 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.59 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.42 (0.24), residues: 1061 helix: -1.46 (0.24), residues: 420 sheet: -2.75 (0.56), residues: 68 loop : -2.93 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 581 TYR 0.034 0.003 TYR C 462 PHE 0.026 0.002 PHE C 381 TRP 0.046 0.003 TRP C 575 HIS 0.016 0.003 HIS C 96 Details of bonding type rmsd covalent geometry : bond 0.01734 ( 8869) covalent geometry : angle 0.84942 (12004) hydrogen bonds : bond 0.04802 ( 330) hydrogen bonds : angle 6.88252 ( 897) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.3001 (mmm) cc_final: 0.2772 (mmm) REVERT: C 213 GLU cc_start: 0.8937 (mp0) cc_final: 0.8241 (tm-30) REVERT: C 414 LEU cc_start: 0.8019 (mt) cc_final: 0.7751 (mt) REVERT: C 526 LEU cc_start: 0.8868 (mt) cc_final: 0.8649 (mt) REVERT: C 726 MET cc_start: 0.9355 (mmm) cc_final: 0.9112 (mmm) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2486 time to fit residues: 30.7196 Evaluate side-chains 82 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 59 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.089367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.063302 restraints weight = 197095.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.067266 restraints weight = 121859.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.069821 restraints weight = 84280.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.071072 restraints weight = 64244.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.072226 restraints weight = 55222.502| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.5804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.108 8869 Z= 0.668 Angle : 0.810 16.971 12004 Z= 0.434 Chirality : 0.049 0.434 1314 Planarity : 0.007 0.150 1564 Dihedral : 8.735 38.052 1165 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 24.30 Ramachandran Plot: Outliers : 0.28 % Allowed : 14.70 % Favored : 85.01 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.35 (0.24), residues: 1061 helix: -1.42 (0.24), residues: 422 sheet: -2.73 (0.55), residues: 68 loop : -2.87 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 581 TYR 0.032 0.003 TYR C 462 PHE 0.039 0.002 PHE C 381 TRP 0.034 0.003 TRP C 575 HIS 0.009 0.002 HIS C 778 Details of bonding type rmsd covalent geometry : bond 0.01715 ( 8869) covalent geometry : angle 0.80980 (12004) hydrogen bonds : bond 0.04491 ( 330) hydrogen bonds : angle 6.74300 ( 897) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4350.26 seconds wall clock time: 74 minutes 53.56 seconds (4493.56 seconds total)