Starting phenix.real_space_refine on Thu Oct 22 19:38:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sf8_54816/10_2026/9sf8_54816.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sf8_54816/10_2026/9sf8_54816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sf8_54816/10_2026/9sf8_54816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sf8_54816/10_2026/9sf8_54816.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sf8_54816/10_2026/9sf8_54816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sf8_54816/10_2026/9sf8_54816.map" } resolution = 2.6 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= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 11 5.16 5 C 2737 2.51 5 N 755 2.21 5 O 852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4355 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4355 Classifications: {'peptide': 562} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 536} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 1.28, per 1000 atoms: 0.29 Number of scatterers: 4355 At special positions: 0 Unit cell: (62.7, 63.84, 103.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 11 16.00 O 852 8.00 N 755 7.00 C 2737 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 171.9 milliseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1034 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 8 sheets defined 16.9% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 Processing helix chain 'A' and resid 139 through 146 Processing helix chain 'A' and resid 279 through 293 Processing helix chain 'A' and resid 319 through 333 removed outlier: 3.729A pdb=" N LEU A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 447 through 469 removed outlier: 4.156A pdb=" N GLN A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG A 452 " --> pdb=" O LYS A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 494 Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 546 through 550 removed outlier: 3.552A pdb=" N GLY A 550 " --> pdb=" O GLU A 547 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 31 removed outlier: 6.603A pdb=" N TYR A 38 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU A 31 " --> pdb=" O HIS A 36 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N HIS A 36 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N GLY A 53 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N ILE A 96 " --> pdb=" O GLY A 53 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG A 55 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ALA A 98 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE A 57 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ALA A 100 " --> pdb=" O PHE A 57 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N SER A 72 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A 101 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N THR A 70 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N LYS A 103 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL A 68 " --> pdb=" O LYS A 103 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP A 67 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 26 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE A 71 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLU A 24 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY A 73 " --> pdb=" O THR A 22 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N THR A 22 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL A 75 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ALA A 20 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 114 removed outlier: 6.110A pdb=" N LEU A 113 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ASP A 155 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL A 233 " --> pdb=" O PRO A 198 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU A 200 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 215 Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 341 removed outlier: 6.972A pdb=" N GLY A 361 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE A 303 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU A 363 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLY A 301 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER A 262 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N GLY A 301 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA A 264 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ILE A 303 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TYR A 266 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL A 305 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N ILE A 268 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 370 through 371 Processing sheet with id=AA6, first strand: chain 'A' and resid 370 through 371 removed outlier: 4.034A pdb=" N ASN A 473 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE A 474 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 385 through 386 Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 514 139 hydrogen bonds defined for protein. 348 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.75 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1481 1.34 - 1.46: 589 1.46 - 1.57: 2346 1.57 - 1.69: 0 1.69 - 1.81: 21 Bond restraints: 4437 Sorted by residual: bond pdb=" CG ARG A 359 " pdb=" CD ARG A 359 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.39e-01 bond pdb=" CB THR A 317 " pdb=" CG2 THR A 317 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.39e-01 bond pdb=" CG LEU A 477 " pdb=" CD2 LEU A 477 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.89e-01 bond pdb=" CB ARG A 551 " pdb=" CG ARG A 551 " ideal model delta sigma weight residual 1.520 1.499 0.021 3.00e-02 1.11e+03 4.82e-01 bond pdb=" CG PRO A 544 " pdb=" CD PRO A 544 " ideal model delta sigma weight residual 1.503 1.479 0.024 3.40e-02 8.65e+02 4.79e-01 ... (remaining 4432 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 5725 1.08 - 2.16: 237 2.16 - 3.24: 39 3.24 - 4.32: 7 4.32 - 5.40: 5 Bond angle restraints: 6013 Sorted by residual: angle pdb=" C ALA A 123 " pdb=" N ASN A 124 " pdb=" CA ASN A 124 " ideal model delta sigma weight residual 121.54 126.73 -5.19 1.91e+00 2.74e-01 7.39e+00 angle pdb=" C ASP A 307 " pdb=" CA ASP A 307 " pdb=" CB ASP A 307 " ideal model delta sigma weight residual 112.99 108.89 4.10 2.10e+00 2.27e-01 3.81e+00 angle pdb=" N ASN A 124 " pdb=" CA ASN A 124 " pdb=" C ASN A 124 " ideal model delta sigma weight residual 110.80 114.22 -3.42 2.13e+00 2.20e-01 2.58e+00 angle pdb=" N THR A 89 " pdb=" CA THR A 89 " pdb=" C THR A 89 " ideal model delta sigma weight residual 110.80 114.16 -3.36 2.13e+00 2.20e-01 2.48e+00 angle pdb=" CA ASN A 124 " pdb=" C ASN A 124 " pdb=" N ILE A 125 " ideal model delta sigma weight residual 116.84 119.45 -2.61 1.71e+00 3.42e-01 2.32e+00 ... (remaining 6008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 2362 17.83 - 35.66: 232 35.66 - 53.49: 76 53.49 - 71.32: 7 71.32 - 89.14: 6 Dihedral angle restraints: 2683 sinusoidal: 1070 harmonic: 1613 Sorted by residual: dihedral pdb=" CA ILE A 268 " pdb=" C ILE A 268 " pdb=" N GLU A 269 " pdb=" CA GLU A 269 " ideal model delta harmonic sigma weight residual 180.00 162.61 17.39 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CB GLU A 346 " pdb=" CG GLU A 346 " pdb=" CD GLU A 346 " pdb=" OE1 GLU A 346 " ideal model delta sinusoidal sigma weight residual 0.00 89.14 -89.14 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA ALA A 123 " pdb=" C ALA A 123 " pdb=" N ASN A 124 " pdb=" CA ASN A 124 " ideal model delta harmonic sigma weight residual 180.00 164.27 15.73 0 5.00e+00 4.00e-02 9.90e+00 ... (remaining 2680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 343 0.025 - 0.051: 169 0.051 - 0.076: 86 0.076 - 0.102: 45 0.102 - 0.127: 31 Chirality restraints: 674 Sorted by residual: chirality pdb=" CA ILE A 524 " pdb=" N ILE A 524 " pdb=" C ILE A 524 " pdb=" CB ILE A 524 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA VAL A 231 " pdb=" N VAL A 231 " pdb=" C VAL A 231 " pdb=" CB VAL A 231 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA ILE A 93 " pdb=" N ILE A 93 " pdb=" C ILE A 93 " pdb=" CB ILE A 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 671 not shown) Planarity restraints: 796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 455 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C VAL A 455 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 455 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 456 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 463 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.39e+00 pdb=" C PHE A 463 " 0.027 2.00e-02 2.50e+03 pdb=" O PHE A 463 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA A 464 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 462 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C GLN A 462 " 0.023 2.00e-02 2.50e+03 pdb=" O GLN A 462 " -0.009 2.00e-02 2.50e+03 pdb=" N PHE A 463 " -0.008 2.00e-02 2.50e+03 ... (remaining 793 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.02: 2502 3.02 - 3.49: 4250 3.49 - 3.96: 7644 3.96 - 4.43: 9074 4.43 - 4.90: 14136 Nonbonded interactions: 37606 Sorted by model distance: nonbonded pdb=" N ASP A 554 " pdb=" OD1 ASP A 554 " model vdw 2.555 3.120 nonbonded pdb=" N GLU A 85 " pdb=" OE1 GLU A 85 " model vdw 2.596 3.120 nonbonded pdb=" N ASP A 135 " pdb=" OD1 ASP A 135 " model vdw 2.612 3.120 nonbonded pdb=" N SER A 553 " pdb=" O SER A 553 " model vdw 2.624 2.496 nonbonded pdb=" O PRO A 122 " pdb=" OG1 THR A 194 " model vdw 2.640 3.040 ... (remaining 37601 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.210 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4437 Z= 0.150 Angle : 0.530 5.400 6013 Z= 0.291 Chirality : 0.045 0.127 674 Planarity : 0.003 0.034 796 Dihedral : 16.230 89.144 1649 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.05 % Allowed : 20.75 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 are not related in a simple way. whole: -0.15 (0.35), residues: 560 helix: -0.35 (0.56), residues: 77 sheet: -0.72 (0.40), residues: 139 loop : 0.40 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 86 TYR 0.007 0.001 TYR A 224 PHE 0.022 0.001 PHE A 78 TRP 0.006 0.001 TRP A 404 HIS 0.002 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 4437) covalent geometry : angle 0.53019 / 0.29 ( 6013) hydrogen bonds : bond 0.12933 / 9.08 ( 137) hydrogen bonds : angle 6.85885 / 4.64 ( 348) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.167 Fit side-chains REVERT: A 6 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7721 (mt-10) REVERT: A 64 GLN cc_start: 0.8044 (mt0) cc_final: 0.7472 (mp10) REVERT: A 69 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7368 (mt) REVERT: A 81 ARG cc_start: 0.7842 (mtt180) cc_final: 0.7337 (mpp-170) REVERT: A 85 GLU cc_start: 0.7841 (pm20) cc_final: 0.7467 (mp0) REVERT: A 99 LYS cc_start: 0.8284 (tttm) cc_final: 0.7599 (ttpt) REVERT: A 138 GLU cc_start: 0.8707 (tt0) cc_final: 0.8266 (tt0) REVERT: A 181 ASN cc_start: 0.8687 (p0) cc_final: 0.8446 (p0) REVERT: A 215 LYS cc_start: 0.7897 (tttt) cc_final: 0.7666 (tptt) REVERT: A 256 LYS cc_start: 0.7334 (ttmt) cc_final: 0.6767 (tppp) REVERT: A 279 LYS cc_start: 0.8102 (mttt) cc_final: 0.7602 (mmtp) REVERT: A 281 GLU cc_start: 0.7336 (mp0) cc_final: 0.7106 (mp0) REVERT: A 284 LYS cc_start: 0.7656 (tttt) cc_final: 0.7053 (mppt) REVERT: A 331 LYS cc_start: 0.7622 (tttt) cc_final: 0.7394 (mppt) REVERT: A 333 LEU cc_start: 0.8148 (mt) cc_final: 0.7904 (mp) REVERT: A 348 ASN cc_start: 0.8332 (m-40) cc_final: 0.8039 (m-40) REVERT: A 420 ARG cc_start: 0.6510 (mtp180) cc_final: 0.4847 (mpt180) REVERT: A 433 ARG cc_start: 0.7576 (ttp80) cc_final: 0.6817 (ttp-110) REVERT: A 448 LYS cc_start: 0.7991 (ttpt) cc_final: 0.7510 (mmtt) REVERT: A 462 GLN cc_start: 0.7135 (tt0) cc_final: 0.6790 (mm110) REVERT: A 465 LYS cc_start: 0.7196 (ttpt) cc_final: 0.6805 (ttmm) REVERT: A 538 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7786 (mtt) outliers start: 5 outliers final: 3 residues processed: 74 average time/residue: 0.7369 time to fit residues: 56.1079 Evaluate side-chains 74 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 538 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: [54, 24, 48, 26, 2, 16, 32, 31, 25, 50, 53] chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.138167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.121704 restraints weight = 4691.047| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.56 r_work: 0.3232 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.0599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4437 Z= 0.169 Angle : 0.520 5.604 6013 Z= 0.276 Chirality : 0.046 0.133 674 Planarity : 0.003 0.033 796 Dihedral : 5.858 50.205 613 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.94 % Allowed : 18.87 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 are not related in a simple way. whole: 0.25 (0.36), residues: 560 helix: 0.73 (0.60), residues: 79 sheet: -0.50 (0.41), residues: 131 loop : 0.45 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 368 TYR 0.008 0.001 TYR A 224 PHE 0.014 0.001 PHE A 78 TRP 0.005 0.001 TRP A 404 HIS 0.002 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 4437) covalent geometry : angle 0.51960 / 0.28 ( 6013) hydrogen bonds : bond 0.04879 / 3.35 ( 137) hydrogen bonds : angle 5.22940 / 3.43 ( 348) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.179 Fit side-chains REVERT: A 3 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7160 (mttm) REVERT: A 6 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7658 (mt-10) REVERT: A 64 GLN cc_start: 0.8094 (mt0) cc_final: 0.7540 (mp10) REVERT: A 81 ARG cc_start: 0.7923 (mtt180) cc_final: 0.7443 (mpp-170) REVERT: A 99 LYS cc_start: 0.8152 (tttm) cc_final: 0.7575 (ttpt) REVERT: A 181 ASN cc_start: 0.8804 (p0) cc_final: 0.8557 (p0) REVERT: A 215 LYS cc_start: 0.7815 (tttt) cc_final: 0.7612 (tptt) REVERT: A 239 MET cc_start: 0.8990 (mmm) cc_final: 0.8681 (mmm) REVERT: A 256 LYS cc_start: 0.7377 (ttmt) cc_final: 0.6965 (tppp) REVERT: A 279 LYS cc_start: 0.7927 (mttt) cc_final: 0.7505 (mmtt) REVERT: A 281 GLU cc_start: 0.7487 (mp0) cc_final: 0.7227 (mp0) REVERT: A 284 LYS cc_start: 0.7718 (tttt) cc_final: 0.7126 (mppt) REVERT: A 333 LEU cc_start: 0.8008 (mt) cc_final: 0.7750 (mp) REVERT: A 348 ASN cc_start: 0.8354 (m-40) cc_final: 0.8082 (m-40) REVERT: A 420 ARG cc_start: 0.6175 (mtp180) cc_final: 0.4538 (mpt180) REVERT: A 433 ARG cc_start: 0.7590 (ttp80) cc_final: 0.6825 (ttp-110) REVERT: A 448 LYS cc_start: 0.7849 (ttpt) cc_final: 0.7495 (mmtt) REVERT: A 462 GLN cc_start: 0.7660 (tt0) cc_final: 0.7314 (mm110) REVERT: A 465 LYS cc_start: 0.7552 (ttpt) cc_final: 0.7090 (ttmm) REVERT: A 497 MET cc_start: 0.9044 (mmm) cc_final: 0.8689 (mmm) outliers start: 14 outliers final: 7 residues processed: 82 average time/residue: 0.6818 time to fit residues: 57.6183 Evaluate side-chains 75 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 505 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: [1, 51, 38, 10, 21, 11, 25, 14, 37, 35, 52] chunk 1 optimal weight: 0.0000 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.137007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120693 restraints weight = 4724.019| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.55 r_work: 0.3229 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4437 Z= 0.175 Angle : 0.526 5.698 6013 Z= 0.278 Chirality : 0.046 0.143 674 Planarity : 0.003 0.033 796 Dihedral : 5.476 48.838 604 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.14 % Allowed : 19.92 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 are not related in a simple way. whole: 0.20 (0.36), residues: 560 helix: 0.63 (0.59), residues: 79 sheet: -0.54 (0.41), residues: 131 loop : 0.44 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.008 0.002 TYR A 143 PHE 0.016 0.002 PHE A 78 TRP 0.008 0.001 TRP A 404 HIS 0.002 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 ( 4437) covalent geometry : angle 0.52624 / 0.28 ( 6013) hydrogen bonds : bond 0.04644 / 3.19 ( 137) hydrogen bonds : angle 5.15123 / 3.35 ( 348) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.180 Fit side-chains REVERT: A 3 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7164 (mttm) REVERT: A 6 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7623 (mt-10) REVERT: A 59 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7050 (mmtt) REVERT: A 64 GLN cc_start: 0.8122 (mt0) cc_final: 0.7576 (mp10) REVERT: A 81 ARG cc_start: 0.7926 (mtt180) cc_final: 0.7482 (mpp-170) REVERT: A 85 GLU cc_start: 0.7840 (pm20) cc_final: 0.7541 (mp0) REVERT: A 99 LYS cc_start: 0.8132 (tttm) cc_final: 0.7537 (ttpt) REVERT: A 102 THR cc_start: 0.8000 (OUTLIER) cc_final: 0.7701 (m) REVERT: A 181 ASN cc_start: 0.8850 (p0) cc_final: 0.8580 (p0) REVERT: A 239 MET cc_start: 0.8927 (mmm) cc_final: 0.8635 (mmm) REVERT: A 256 LYS cc_start: 0.7457 (ttmt) cc_final: 0.6992 (tptm) REVERT: A 279 LYS cc_start: 0.7898 (mttt) cc_final: 0.7457 (mmtt) REVERT: A 284 LYS cc_start: 0.7700 (tttt) cc_final: 0.7110 (mppt) REVERT: A 333 LEU cc_start: 0.7954 (mt) cc_final: 0.7715 (mp) REVERT: A 348 ASN cc_start: 0.8365 (m-40) cc_final: 0.8123 (m-40) REVERT: A 420 ARG cc_start: 0.6318 (mtp180) cc_final: 0.4614 (mpt180) REVERT: A 433 ARG cc_start: 0.7656 (ttp80) cc_final: 0.6907 (ttp-110) REVERT: A 448 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7512 (mmtt) REVERT: A 462 GLN cc_start: 0.7730 (tt0) cc_final: 0.7356 (mm110) REVERT: A 465 LYS cc_start: 0.7534 (ttpt) cc_final: 0.7035 (ttmm) REVERT: A 497 MET cc_start: 0.9080 (mmm) cc_final: 0.8804 (mmm) outliers start: 15 outliers final: 9 residues processed: 75 average time/residue: 0.7180 time to fit residues: 55.4866 Evaluate side-chains 78 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 541 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: [0, 38, 2, 19, 13, 7, 16, 28, 31, 51, 14] chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 0.0050 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.0050 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 overall best weight: 0.5208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.139660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.123579 restraints weight = 4667.688| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.55 r_work: 0.3261 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4437 Z= 0.111 Angle : 0.462 5.411 6013 Z= 0.246 Chirality : 0.044 0.126 674 Planarity : 0.003 0.031 796 Dihedral : 5.113 45.530 604 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.98 % Allowed : 19.92 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 are not related in a simple way. whole: 0.46 (0.36), residues: 560 helix: 0.85 (0.60), residues: 79 sheet: -0.36 (0.42), residues: 124 loop : 0.59 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 452 TYR 0.008 0.001 TYR A 143 PHE 0.012 0.001 PHE A 78 TRP 0.005 0.001 TRP A 404 HIS 0.001 0.000 HIS A 529 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 4437) covalent geometry : angle 0.46174 / 0.25 ( 6013) hydrogen bonds : bond 0.03951 / 2.72 ( 137) hydrogen bonds : angle 4.97892 / 3.21 ( 348) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.213 Fit side-chains REVERT: A 6 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7625 (mt-10) REVERT: A 59 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7018 (mmtt) REVERT: A 64 GLN cc_start: 0.8122 (mt0) cc_final: 0.7600 (mp10) REVERT: A 81 ARG cc_start: 0.7836 (mtt180) cc_final: 0.7403 (mpp-170) REVERT: A 99 LYS cc_start: 0.7994 (tttm) cc_final: 0.7438 (ttpt) REVERT: A 181 ASN cc_start: 0.8660 (p0) cc_final: 0.8423 (p0) REVERT: A 239 MET cc_start: 0.8946 (mmm) cc_final: 0.8688 (mmm) REVERT: A 256 LYS cc_start: 0.7451 (ttmt) cc_final: 0.6987 (tptm) REVERT: A 279 LYS cc_start: 0.7950 (mttt) cc_final: 0.7578 (mmtt) REVERT: A 284 LYS cc_start: 0.7756 (tttt) cc_final: 0.7169 (mppt) REVERT: A 348 ASN cc_start: 0.8316 (m-40) cc_final: 0.8061 (m-40) REVERT: A 420 ARG cc_start: 0.6330 (mtp180) cc_final: 0.5906 (ttp-170) REVERT: A 433 ARG cc_start: 0.7532 (ttp80) cc_final: 0.6796 (ttp-110) REVERT: A 448 LYS cc_start: 0.7818 (ttpt) cc_final: 0.7509 (mmtt) REVERT: A 462 GLN cc_start: 0.7710 (tt0) cc_final: 0.7372 (mm110) REVERT: A 465 LYS cc_start: 0.7525 (ttpt) cc_final: 0.7003 (ttmm) REVERT: A 497 MET cc_start: 0.9093 (mmm) cc_final: 0.8763 (mmm) REVERT: A 547 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7084 (mp0) outliers start: 19 outliers final: 9 residues processed: 80 average time/residue: 0.7038 time to fit residues: 58.1286 Evaluate side-chains 75 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 541 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: [47, 51, 17, 52, 36, 46, 43, 0, 8, 54, 16] chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 470 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.136948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120650 restraints weight = 4771.664| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.57 r_work: 0.3238 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4437 Z= 0.166 Angle : 0.512 5.573 6013 Z= 0.268 Chirality : 0.046 0.130 674 Planarity : 0.003 0.032 796 Dihedral : 4.479 17.426 601 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.98 % Allowed : 20.34 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 are not related in a simple way. whole: 0.23 (0.36), residues: 560 helix: 0.69 (0.60), residues: 79 sheet: -0.52 (0.41), residues: 132 loop : 0.45 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.008 0.001 TYR A 143 PHE 0.017 0.001 PHE A 78 TRP 0.008 0.001 TRP A 404 HIS 0.002 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 4437) covalent geometry : angle 0.51212 / 0.27 ( 6013) hydrogen bonds : bond 0.04276 / 2.93 ( 137) hydrogen bonds : angle 5.01158 / 3.24 ( 348) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.190 Fit side-chains REVERT: A 6 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7629 (mt-10) REVERT: A 59 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7077 (mmtt) REVERT: A 64 GLN cc_start: 0.8119 (mt0) cc_final: 0.7603 (mp10) REVERT: A 81 ARG cc_start: 0.7981 (mtt180) cc_final: 0.7544 (mpp-170) REVERT: A 85 GLU cc_start: 0.7437 (mp0) cc_final: 0.7101 (pm20) REVERT: A 99 LYS cc_start: 0.8080 (tttm) cc_final: 0.7511 (ttpt) REVERT: A 102 THR cc_start: 0.7981 (m) cc_final: 0.7681 (m) REVERT: A 181 ASN cc_start: 0.8689 (p0) cc_final: 0.8480 (p0) REVERT: A 239 MET cc_start: 0.8963 (mmm) cc_final: 0.8728 (mmm) REVERT: A 256 LYS cc_start: 0.7487 (ttmt) cc_final: 0.7024 (tptm) REVERT: A 279 LYS cc_start: 0.7972 (mttt) cc_final: 0.7577 (mmtt) REVERT: A 284 LYS cc_start: 0.7754 (tttt) cc_final: 0.7141 (mppt) REVERT: A 348 ASN cc_start: 0.8345 (m-40) cc_final: 0.8086 (m-40) REVERT: A 420 ARG cc_start: 0.6203 (mtp180) cc_final: 0.5802 (ttp-170) REVERT: A 433 ARG cc_start: 0.7672 (ttp80) cc_final: 0.6912 (ttp-110) REVERT: A 448 LYS cc_start: 0.7841 (ttpt) cc_final: 0.7444 (mmtt) REVERT: A 462 GLN cc_start: 0.7801 (tt0) cc_final: 0.7421 (mm110) REVERT: A 465 LYS cc_start: 0.7637 (ttpt) cc_final: 0.7085 (ttmm) REVERT: A 497 MET cc_start: 0.9093 (mmm) cc_final: 0.8777 (mmm) REVERT: A 538 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7406 (mtt) REVERT: A 547 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7142 (mp0) REVERT: A 560 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8484 (tp) outliers start: 19 outliers final: 11 residues processed: 77 average time/residue: 0.6802 time to fit residues: 54.0094 Evaluate side-chains 81 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 560 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: [17, 23, 9, 37, 6, 1, 28, 3, 21, 46, 7] chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 0.0970 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.139317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.123088 restraints weight = 4781.336| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.57 r_work: 0.3257 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4437 Z= 0.121 Angle : 0.478 5.424 6013 Z= 0.252 Chirality : 0.045 0.161 674 Planarity : 0.003 0.031 796 Dihedral : 4.290 17.546 601 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.77 % Allowed : 20.34 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 are not related in a simple way. whole: 0.22 (0.36), residues: 560 helix: 0.74 (0.59), residues: 81 sheet: -0.49 (0.41), residues: 132 loop : 0.41 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.008 0.001 TYR A 143 PHE 0.014 0.001 PHE A 78 TRP 0.006 0.001 TRP A 404 HIS 0.001 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 4437) covalent geometry : angle 0.47801 / 0.25 ( 6013) hydrogen bonds : bond 0.03908 / 2.68 ( 137) hydrogen bonds : angle 4.94246 / 3.19 ( 348) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.173 Fit side-chains REVERT: A 6 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7589 (mt-10) REVERT: A 59 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7053 (mmtt) REVERT: A 64 GLN cc_start: 0.8124 (mt0) cc_final: 0.7631 (mp10) REVERT: A 81 ARG cc_start: 0.7929 (mtt180) cc_final: 0.7487 (mpp-170) REVERT: A 85 GLU cc_start: 0.7427 (mp0) cc_final: 0.7127 (pm20) REVERT: A 99 LYS cc_start: 0.8014 (tttm) cc_final: 0.7454 (ttpt) REVERT: A 181 ASN cc_start: 0.8665 (p0) cc_final: 0.8426 (p0) REVERT: A 239 MET cc_start: 0.8940 (mmm) cc_final: 0.8732 (mmm) REVERT: A 256 LYS cc_start: 0.7461 (ttmt) cc_final: 0.7000 (tptm) REVERT: A 279 LYS cc_start: 0.7961 (mttt) cc_final: 0.7606 (mmtt) REVERT: A 284 LYS cc_start: 0.7765 (tttt) cc_final: 0.7181 (mppt) REVERT: A 348 ASN cc_start: 0.8329 (m-40) cc_final: 0.8066 (m-40) REVERT: A 420 ARG cc_start: 0.6246 (mtp180) cc_final: 0.5899 (mtp180) REVERT: A 433 ARG cc_start: 0.7628 (ttp80) cc_final: 0.6906 (ttp-110) REVERT: A 448 LYS cc_start: 0.7847 (ttpt) cc_final: 0.7483 (mmtm) REVERT: A 462 GLN cc_start: 0.7757 (tt0) cc_final: 0.7416 (mm110) REVERT: A 465 LYS cc_start: 0.7595 (ttpt) cc_final: 0.7066 (ttmm) REVERT: A 497 MET cc_start: 0.9105 (mmm) cc_final: 0.8796 (mmm) REVERT: A 538 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7336 (mtt) REVERT: A 547 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7185 (mp0) outliers start: 18 outliers final: 11 residues processed: 77 average time/residue: 0.6885 time to fit residues: 54.7340 Evaluate side-chains 82 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 541 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: [22, 1, 21, 28, 47, 14, 31, 50, 15, 46, 41] chunk 22 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.139521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.123236 restraints weight = 4769.981| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.58 r_work: 0.3258 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4437 Z= 0.123 Angle : 0.477 5.444 6013 Z= 0.252 Chirality : 0.045 0.130 674 Planarity : 0.003 0.031 796 Dihedral : 4.272 17.273 601 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.98 % Allowed : 20.13 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 are not related in a simple way. whole: 0.27 (0.36), residues: 560 helix: 0.74 (0.59), residues: 81 sheet: -0.47 (0.42), residues: 132 loop : 0.46 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 396 TYR 0.008 0.001 TYR A 143 PHE 0.015 0.001 PHE A 78 TRP 0.006 0.001 TRP A 404 HIS 0.001 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 4437) covalent geometry : angle 0.47739 / 0.25 ( 6013) hydrogen bonds : bond 0.03900 / 2.67 ( 137) hydrogen bonds : angle 4.92559 / 3.17 ( 348) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.192 Fit side-chains REVERT: A 6 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7601 (mt-10) REVERT: A 59 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7023 (mmtt) REVERT: A 64 GLN cc_start: 0.8125 (mt0) cc_final: 0.7655 (mp10) REVERT: A 81 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7472 (mpp-170) REVERT: A 85 GLU cc_start: 0.7434 (mp0) cc_final: 0.7131 (pm20) REVERT: A 99 LYS cc_start: 0.7948 (tttm) cc_final: 0.7451 (ttpt) REVERT: A 102 THR cc_start: 0.7966 (OUTLIER) cc_final: 0.7646 (m) REVERT: A 181 ASN cc_start: 0.8651 (p0) cc_final: 0.8422 (p0) REVERT: A 256 LYS cc_start: 0.7454 (ttmt) cc_final: 0.6910 (tppp) REVERT: A 279 LYS cc_start: 0.7954 (mttt) cc_final: 0.7586 (mmtt) REVERT: A 284 LYS cc_start: 0.7759 (tttt) cc_final: 0.7168 (mppt) REVERT: A 348 ASN cc_start: 0.8347 (m-40) cc_final: 0.8029 (m-40) REVERT: A 433 ARG cc_start: 0.7653 (ttp80) cc_final: 0.6904 (ttp-110) REVERT: A 448 LYS cc_start: 0.7872 (ttpt) cc_final: 0.7478 (mmtm) REVERT: A 462 GLN cc_start: 0.7791 (tt0) cc_final: 0.7402 (mm110) REVERT: A 465 LYS cc_start: 0.7603 (ttpt) cc_final: 0.7058 (ttmm) REVERT: A 497 MET cc_start: 0.9094 (mmm) cc_final: 0.8756 (mmm) REVERT: A 538 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7347 (mtt) REVERT: A 547 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7192 (mp0) REVERT: A 560 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8450 (tp) outliers start: 19 outliers final: 11 residues processed: 80 average time/residue: 0.6674 time to fit residues: 55.0857 Evaluate side-chains 83 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 560 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: [36, 6, 5, 31, 46, 52, 53, 10, 23, 19, 12] chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 46 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 23 optimal weight: 0.0770 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 470 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.121595 restraints weight = 4748.598| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.57 r_work: 0.3247 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4437 Z= 0.162 Angle : 0.518 5.532 6013 Z= 0.271 Chirality : 0.046 0.130 674 Planarity : 0.003 0.032 796 Dihedral : 4.453 17.461 601 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.77 % Allowed : 20.75 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 are not related in a simple way. whole: 0.22 (0.36), residues: 560 helix: 0.71 (0.60), residues: 79 sheet: -0.53 (0.42), residues: 132 loop : 0.44 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.008 0.001 TYR A 224 PHE 0.017 0.001 PHE A 78 TRP 0.007 0.001 TRP A 404 HIS 0.001 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 4437) covalent geometry : angle 0.51783 / 0.27 ( 6013) hydrogen bonds : bond 0.04194 / 2.87 ( 137) hydrogen bonds : angle 5.03301 / 3.25 ( 348) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.184 Fit side-chains REVERT: A 6 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7698 (mt-10) REVERT: A 59 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7043 (mmtt) REVERT: A 64 GLN cc_start: 0.8157 (mt0) cc_final: 0.7631 (mp10) REVERT: A 81 ARG cc_start: 0.8009 (mtt180) cc_final: 0.7579 (mpp-170) REVERT: A 85 GLU cc_start: 0.7461 (mp0) cc_final: 0.7149 (pm20) REVERT: A 99 LYS cc_start: 0.8009 (tttm) cc_final: 0.7521 (ttpt) REVERT: A 102 THR cc_start: 0.7990 (m) cc_final: 0.7688 (m) REVERT: A 181 ASN cc_start: 0.8690 (p0) cc_final: 0.8469 (p0) REVERT: A 256 LYS cc_start: 0.7391 (ttmt) cc_final: 0.6876 (tppp) REVERT: A 279 LYS cc_start: 0.7966 (mttt) cc_final: 0.7608 (mmtp) REVERT: A 284 LYS cc_start: 0.7747 (tttt) cc_final: 0.7143 (mppt) REVERT: A 348 ASN cc_start: 0.8410 (m-40) cc_final: 0.8097 (m-40) REVERT: A 433 ARG cc_start: 0.7676 (ttp80) cc_final: 0.6926 (ttp-110) REVERT: A 448 LYS cc_start: 0.7899 (ttpt) cc_final: 0.7498 (mmtm) REVERT: A 462 GLN cc_start: 0.7834 (tt0) cc_final: 0.7426 (mm110) REVERT: A 465 LYS cc_start: 0.7571 (ttpt) cc_final: 0.6982 (ttmm) REVERT: A 497 MET cc_start: 0.9094 (mmm) cc_final: 0.8760 (mmm) REVERT: A 538 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7431 (mtt) REVERT: A 547 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7162 (mp0) outliers start: 18 outliers final: 12 residues processed: 77 average time/residue: 0.6347 time to fit residues: 50.4690 Evaluate side-chains 81 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 532 ASP Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 541 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: [6, 39, 35, 30, 53, 8, 21, 37, 12, 55, 28] chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.137541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.121237 restraints weight = 4791.899| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.58 r_work: 0.3236 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4437 Z= 0.166 Angle : 0.527 5.548 6013 Z= 0.276 Chirality : 0.046 0.127 674 Planarity : 0.003 0.031 796 Dihedral : 4.501 17.954 601 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.56 % Allowed : 21.17 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 are not related in a simple way. whole: 0.17 (0.36), residues: 560 helix: 0.61 (0.59), residues: 79 sheet: -0.55 (0.42), residues: 132 loop : 0.42 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.008 0.001 TYR A 143 PHE 0.015 0.001 PHE A 78 TRP 0.005 0.001 TRP A 404 HIS 0.002 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 4437) covalent geometry : angle 0.52661 / 0.28 ( 6013) hydrogen bonds : bond 0.04231 / 2.89 ( 137) hydrogen bonds : angle 5.08960 / 3.29 ( 348) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.203 Fit side-chains REVERT: A 6 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 59 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7062 (mmtt) REVERT: A 64 GLN cc_start: 0.8139 (mt0) cc_final: 0.7634 (mp10) REVERT: A 81 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7615 (mpp-170) REVERT: A 85 GLU cc_start: 0.7458 (mp0) cc_final: 0.7157 (pm20) REVERT: A 99 LYS cc_start: 0.7989 (tttm) cc_final: 0.7462 (ttpt) REVERT: A 102 THR cc_start: 0.8024 (m) cc_final: 0.7717 (m) REVERT: A 181 ASN cc_start: 0.8736 (p0) cc_final: 0.8507 (p0) REVERT: A 256 LYS cc_start: 0.7473 (ttmt) cc_final: 0.6924 (tppp) REVERT: A 279 LYS cc_start: 0.7961 (mttt) cc_final: 0.7617 (mmtp) REVERT: A 284 LYS cc_start: 0.7754 (tttt) cc_final: 0.7149 (mppt) REVERT: A 348 ASN cc_start: 0.8359 (m-40) cc_final: 0.8107 (m-40) REVERT: A 433 ARG cc_start: 0.7642 (ttp80) cc_final: 0.6910 (ttp-110) REVERT: A 448 LYS cc_start: 0.7885 (ttpt) cc_final: 0.7494 (mmtm) REVERT: A 462 GLN cc_start: 0.7793 (tt0) cc_final: 0.7417 (mm110) REVERT: A 465 LYS cc_start: 0.7552 (ttpt) cc_final: 0.6970 (ttmm) REVERT: A 497 MET cc_start: 0.9085 (mmm) cc_final: 0.8752 (mmm) REVERT: A 538 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7440 (mtt) REVERT: A 547 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7198 (mp0) outliers start: 17 outliers final: 12 residues processed: 77 average time/residue: 0.6313 time to fit residues: 50.1862 Evaluate side-chains 80 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 541 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: [7, 18, 24, 14, 39, 19, 27, 10, 47, 48, 46] chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.0050 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 0.0370 chunk 19 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.4272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.124795 restraints weight = 4684.658| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.54 r_work: 0.3289 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4437 Z= 0.105 Angle : 0.475 7.086 6013 Z= 0.250 Chirality : 0.044 0.145 674 Planarity : 0.003 0.030 796 Dihedral : 4.194 17.196 601 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.94 % Allowed : 21.80 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 are not related in a simple way. whole: 0.41 (0.36), residues: 560 helix: 0.66 (0.60), residues: 81 sheet: -0.34 (0.43), residues: 124 loop : 0.56 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 132 TYR 0.008 0.001 TYR A 143 PHE 0.009 0.001 PHE A 78 TRP 0.004 0.001 TRP A 404 HIS 0.001 0.001 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 ( 4437) covalent geometry : angle 0.47467 / 0.25 ( 6013) hydrogen bonds : bond 0.03817 / 2.62 ( 137) hydrogen bonds : angle 4.98131 / 3.20 ( 348) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.143 Fit side-chains REVERT: A 6 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7624 (mt-10) REVERT: A 59 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7031 (mmtt) REVERT: A 64 GLN cc_start: 0.8142 (mt0) cc_final: 0.7634 (mp10) REVERT: A 81 ARG cc_start: 0.7944 (mtt180) cc_final: 0.7637 (mpp-170) REVERT: A 85 GLU cc_start: 0.7417 (mp0) cc_final: 0.7140 (pm20) REVERT: A 99 LYS cc_start: 0.7999 (tttm) cc_final: 0.7545 (ttpt) REVERT: A 102 THR cc_start: 0.7959 (m) cc_final: 0.7629 (m) REVERT: A 181 ASN cc_start: 0.8632 (p0) cc_final: 0.8388 (p0) REVERT: A 256 LYS cc_start: 0.7438 (ttmt) cc_final: 0.6883 (tppp) REVERT: A 279 LYS cc_start: 0.7987 (mttt) cc_final: 0.7630 (mmtp) REVERT: A 284 LYS cc_start: 0.7761 (tttt) cc_final: 0.7189 (mppt) REVERT: A 317 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.8140 (t) REVERT: A 331 LYS cc_start: 0.7712 (mppt) cc_final: 0.7388 (mtpt) REVERT: A 348 ASN cc_start: 0.8290 (m-40) cc_final: 0.7954 (m-40) REVERT: A 420 ARG cc_start: 0.6436 (mtp180) cc_final: 0.6151 (mtp180) REVERT: A 433 ARG cc_start: 0.7554 (ttp80) cc_final: 0.6855 (ttp-110) REVERT: A 448 LYS cc_start: 0.7811 (ttpt) cc_final: 0.7471 (mmtt) REVERT: A 462 GLN cc_start: 0.7762 (tt0) cc_final: 0.7396 (mm110) REVERT: A 465 LYS cc_start: 0.7560 (ttpt) cc_final: 0.7012 (ttmm) REVERT: A 497 MET cc_start: 0.9040 (mmm) cc_final: 0.8668 (mmm) REVERT: A 499 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8456 (t0) REVERT: A 547 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7096 (mp0) outliers start: 14 outliers final: 6 residues processed: 78 average time/residue: 0.6225 time to fit residues: 50.1439 Evaluate side-chains 78 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 541 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: [25, 4, 10, 5, 48, 21, 16, 23, 47, 32, 37] chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.133470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.117012 restraints weight = 4866.674| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.58 r_work: 0.3199 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 4437 Z= 0.324 Angle : 0.680 6.556 6013 Z= 0.354 Chirality : 0.052 0.149 674 Planarity : 0.005 0.043 796 Dihedral : 5.042 18.454 601 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.52 % Allowed : 23.06 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 are not related in a simple way. whole: -0.09 (0.35), residues: 560 helix: 0.21 (0.59), residues: 79 sheet: -0.65 (0.43), residues: 128 loop : 0.25 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 177 TYR 0.013 0.003 TYR A 224 PHE 0.024 0.002 PHE A 78 TRP 0.011 0.002 TRP A 404 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00780 / 0.32 ( 4437) covalent geometry : angle 0.67987 / 0.35 ( 6013) hydrogen bonds : bond 0.05304 / 3.63 ( 137) hydrogen bonds : angle 5.34614 / 3.51 ( 348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1809.12 seconds wall clock time: 31 minutes 35.26 seconds (1895.26 seconds total)