Starting phenix.real_space_refine (version: dev) on Mon Dec 12 11:00:20 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mgv_9112/12_2022/6mgv_9112.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mgv_9112/12_2022/6mgv_9112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mgv_9112/12_2022/6mgv_9112.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mgv_9112/12_2022/6mgv_9112.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mgv_9112/12_2022/6mgv_9112.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mgv_9112/12_2022/6mgv_9112.pdb" } resolution = 3.1 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 10150 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5075 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 34, 'TRANS': 599} Chain breaks: 4 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 5075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5075 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 34, 'TRANS': 599} Chain breaks: 4 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Time building chain proxies: 5.77, per 1000 atoms: 0.57 Number of scatterers: 10150 At special positions: 0 Unit cell: (123.05, 129.95, 95.45, 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 48 16.00 O 1708 8.00 N 1650 7.00 C 6744 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.16 Conformation dependent library (CDL) restraints added in 1.4 seconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2432 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 2 sheets defined 76.9% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 3 through 29 Processing helix chain 'A' and resid 30 through 33 removed outlier: 6.322A pdb=" N PHE A 33 " --> pdb=" O LEU A 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 30 through 33' Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.557A pdb=" N LEU A 80 " --> pdb=" O MET A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 92 through 121 removed outlier: 4.048A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 157 through 195 Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 216 through 229 Processing helix chain 'A' and resid 242 through 269 Processing helix chain 'A' and resid 290 through 313 Processing helix chain 'A' and resid 314 through 317 removed outlier: 6.347A pdb=" N LYS A 317 " --> pdb=" O ASN A 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 314 through 317' Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.710A pdb=" N ILE A 366 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 422 through 438 Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 440 through 452 Processing helix chain 'A' and resid 456 through 476 Processing helix chain 'A' and resid 477 through 489 Processing helix chain 'A' and resid 504 through 512 Proline residue: A 510 - end of helix Processing helix chain 'A' and resid 512 through 524 Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'A' and resid 534 through 548 Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 565 through 584 Proline residue: A 571 - end of helix Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 590 through 612 Processing helix chain 'A' and resid 623 through 646 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 659 through 677 Processing helix chain 'A' and resid 677 through 682 Processing helix chain 'A' and resid 684 through 699 Processing helix chain 'A' and resid 703 through 710 removed outlier: 4.027A pdb=" N ASN A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 29 Processing helix chain 'B' and resid 30 through 33 removed outlier: 6.323A pdb=" N PHE B 33 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.557A pdb=" N LEU B 80 " --> pdb=" O MET B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 92 through 121 removed outlier: 4.048A pdb=" N TYR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 157 through 195 Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 216 through 229 Processing helix chain 'B' and resid 242 through 269 Processing helix chain 'B' and resid 290 through 313 Processing helix chain 'B' and resid 314 through 317 removed outlier: 6.347A pdb=" N LYS B 317 " --> pdb=" O ASN B 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 314 through 317' Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 360 through 366 removed outlier: 3.711A pdb=" N ILE B 366 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 389 through 400 Processing helix chain 'B' and resid 422 through 438 Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 440 through 452 Processing helix chain 'B' and resid 456 through 476 Processing helix chain 'B' and resid 477 through 489 Processing helix chain 'B' and resid 504 through 512 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 512 through 524 Processing helix chain 'B' and resid 524 through 532 Processing helix chain 'B' and resid 534 through 548 Processing helix chain 'B' and resid 554 through 559 Processing helix chain 'B' and resid 565 through 584 Proline residue: B 571 - end of helix Processing helix chain 'B' and resid 587 through 589 No H-bonds generated for 'chain 'B' and resid 587 through 589' Processing helix chain 'B' and resid 590 through 612 Processing helix chain 'B' and resid 623 through 646 Processing helix chain 'B' and resid 654 through 659 Processing helix chain 'B' and resid 659 through 677 Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 684 through 699 Processing helix chain 'B' and resid 703 through 710 removed outlier: 4.027A pdb=" N ASN B 710 " --> pdb=" O GLY B 706 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 240 removed outlier: 5.602A pdb=" N ALA A 322 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 240 removed outlier: 5.602A pdb=" N ALA B 322 " --> pdb=" O VAL B 239 " (cutoff:3.500A) 695 hydrogen bonds defined for protein. 2055 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: 2.87 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2294 1.33 - 1.45: 2924 1.45 - 1.58: 5128 1.58 - 1.70: 6 1.70 - 1.83: 88 Bond restraints: 10440 Sorted by residual: bond pdb=" N PRO B 210 " pdb=" CD PRO B 210 " ideal model delta sigma weight residual 1.473 1.410 0.063 1.40e-02 5.10e+03 2.03e+01 bond pdb=" N PRO A 210 " pdb=" CD PRO A 210 " ideal model delta sigma weight residual 1.473 1.410 0.063 1.40e-02 5.10e+03 2.03e+01 bond pdb=" CB GLN B 615 " pdb=" CG GLN B 615 " ideal model delta sigma weight residual 1.520 1.407 0.113 3.00e-02 1.11e+03 1.43e+01 bond pdb=" CB GLN A 615 " pdb=" CG GLN A 615 " ideal model delta sigma weight residual 1.520 1.407 0.113 3.00e-02 1.11e+03 1.43e+01 bond pdb=" N PRO A 715 " pdb=" CD PRO A 715 " ideal model delta sigma weight residual 1.473 1.424 0.049 1.40e-02 5.10e+03 1.21e+01 ... (remaining 10435 not shown) Histogram of bond angle deviations from ideal: 98.25 - 105.47: 301 105.47 - 112.69: 5188 112.69 - 119.91: 4279 119.91 - 127.13: 4313 127.13 - 134.35: 119 Bond angle restraints: 14200 Sorted by residual: angle pdb=" N SER B 619 " pdb=" CA SER B 619 " pdb=" C SER B 619 " ideal model delta sigma weight residual 110.17 98.84 11.33 1.61e+00 3.86e-01 4.95e+01 angle pdb=" N SER A 619 " pdb=" CA SER A 619 " pdb=" C SER A 619 " ideal model delta sigma weight residual 110.17 98.86 11.31 1.61e+00 3.86e-01 4.94e+01 angle pdb=" N ASP A 554 " pdb=" CA ASP A 554 " pdb=" C ASP A 554 " ideal model delta sigma weight residual 113.17 105.63 7.54 1.26e+00 6.30e-01 3.58e+01 angle pdb=" N ASP B 554 " pdb=" CA ASP B 554 " pdb=" C ASP B 554 " ideal model delta sigma weight residual 113.17 105.68 7.49 1.26e+00 6.30e-01 3.54e+01 angle pdb=" N LYS A 41 " pdb=" CA LYS A 41 " pdb=" C LYS A 41 " ideal model delta sigma weight residual 110.41 103.15 7.26 1.23e+00 6.61e-01 3.48e+01 ... (remaining 14195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.74: 5849 14.74 - 29.49: 209 29.49 - 44.23: 38 44.23 - 58.98: 26 58.98 - 73.72: 6 Dihedral angle restraints: 6128 sinusoidal: 2386 harmonic: 3742 Sorted by residual: dihedral pdb=" CA ASP A 212 " pdb=" CB ASP A 212 " pdb=" CG ASP A 212 " pdb=" OD1 ASP A 212 " ideal model delta sinusoidal sigma weight residual -30.00 -82.32 52.32 1 2.00e+01 2.50e-03 9.33e+00 dihedral pdb=" CA ASP B 212 " pdb=" CB ASP B 212 " pdb=" CG ASP B 212 " pdb=" OD1 ASP B 212 " ideal model delta sinusoidal sigma weight residual -30.00 -82.29 52.29 1 2.00e+01 2.50e-03 9.32e+00 dihedral pdb=" N TYR A 613 " pdb=" C TYR A 613 " pdb=" CA TYR A 613 " pdb=" CB TYR A 613 " ideal model delta harmonic sigma weight residual 122.80 130.19 -7.39 0 2.50e+00 1.60e-01 8.74e+00 ... (remaining 6125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1089 0.075 - 0.150: 401 0.150 - 0.225: 81 0.225 - 0.300: 28 0.300 - 0.375: 5 Chirality restraints: 1604 Sorted by residual: chirality pdb=" CA PHE A 109 " pdb=" N PHE A 109 " pdb=" C PHE A 109 " pdb=" CB PHE A 109 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA PHE B 109 " pdb=" N PHE B 109 " pdb=" C PHE B 109 " pdb=" CB PHE B 109 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CA TYR A 613 " pdb=" N TYR A 613 " pdb=" C TYR A 613 " pdb=" CB TYR A 613 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 1601 not shown) Planarity restraints: 1762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 352 " -0.041 2.00e-02 2.50e+03 1.98e-02 9.81e+00 pdb=" CG TRP B 352 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP B 352 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP B 352 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP B 352 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B 352 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 352 " 0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 352 " -0.023 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 352 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 352 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 519 " 0.036 2.00e-02 2.50e+03 2.20e-02 9.64e+00 pdb=" CG TYR A 519 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR A 519 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 519 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR A 519 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 519 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 519 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR A 519 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 352 " 0.040 2.00e-02 2.50e+03 1.96e-02 9.62e+00 pdb=" CG TRP A 352 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP A 352 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 352 " -0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP A 352 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 352 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 352 " -0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 352 " 0.023 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 352 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 352 " 0.019 2.00e-02 2.50e+03 ... (remaining 1759 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 192 2.65 - 3.21: 10310 3.21 - 3.77: 16551 3.77 - 4.34: 22521 4.34 - 4.90: 36727 Nonbonded interactions: 86301 Sorted by model distance: nonbonded pdb=" NH2 ARG B 330 " pdb=" OE1 GLU B 695 " model vdw 2.082 2.520 nonbonded pdb=" NH2 ARG A 330 " pdb=" OE1 GLU A 695 " model vdw 2.082 2.520 nonbonded pdb=" OH TYR A 167 " pdb=" O PHE A 657 " model vdw 2.212 2.440 nonbonded pdb=" OH TYR B 167 " pdb=" O PHE B 657 " model vdw 2.212 2.440 nonbonded pdb=" NH1 ARG A 330 " pdb=" OE1 GLU A 695 " model vdw 2.272 2.520 ... (remaining 86296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6744 2.51 5 N 1650 2.21 5 O 1708 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.680 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.090 Process input model: 28.250 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 : 0.018 0.113 10440 Z= 1.176 Angle : 1.436 11.328 14200 Z= 0.968 Chirality : 0.084 0.375 1604 Planarity : 0.009 0.039 1762 Dihedral : 9.732 73.722 3696 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.37 % Favored : 96.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.22), residues: 1248 helix: 0.35 (0.16), residues: 880 sheet: -1.04 (0.73), residues: 46 loop : -1.58 (0.32), residues: 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.246 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2538 time to fit residues: 78.2499 Evaluate side-chains 161 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.195 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN A 341 GLN A 363 ASN A 607 HIS A 608 GLN A 614 ASN B 340 GLN B 341 GLN B 363 ASN B 607 HIS B 608 GLN B 614 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10440 Z= 0.225 Angle : 0.610 6.604 14200 Z= 0.327 Chirality : 0.044 0.153 1604 Planarity : 0.005 0.046 1762 Dihedral : 4.711 25.128 1360 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1248 helix: 1.98 (0.17), residues: 854 sheet: -1.26 (0.78), residues: 42 loop : -1.30 (0.32), residues: 352 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 186 time to evaluate : 1.073 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 189 average time/residue: 0.1956 time to fit residues: 54.5819 Evaluate side-chains 153 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 114 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10440 Z= 0.216 Angle : 0.563 5.875 14200 Z= 0.298 Chirality : 0.042 0.146 1604 Planarity : 0.005 0.053 1762 Dihedral : 4.450 24.401 1360 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1248 helix: 2.19 (0.17), residues: 844 sheet: -1.29 (0.75), residues: 46 loop : -1.67 (0.31), residues: 358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 169 time to evaluate : 1.138 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 173 average time/residue: 0.1960 time to fit residues: 49.7877 Evaluate side-chains 160 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 154 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1103 time to fit residues: 2.7802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.0010 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 0.2980 chunk 121 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 HIS B 542 HIS B 615 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 10440 Z= 0.166 Angle : 0.523 6.471 14200 Z= 0.274 Chirality : 0.041 0.135 1604 Planarity : 0.004 0.053 1762 Dihedral : 4.285 24.517 1360 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.24), residues: 1248 helix: 2.26 (0.17), residues: 846 sheet: -1.33 (0.76), residues: 46 loop : -1.65 (0.32), residues: 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 165 time to evaluate : 1.201 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 166 average time/residue: 0.1983 time to fit residues: 48.3062 Evaluate side-chains 160 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 158 time to evaluate : 1.123 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1099 time to fit residues: 1.9656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 3.9990 chunk 69 optimal weight: 0.0870 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.0020 chunk 103 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 10440 Z= 0.177 Angle : 0.531 8.215 14200 Z= 0.274 Chirality : 0.041 0.147 1604 Planarity : 0.004 0.053 1762 Dihedral : 4.204 23.915 1360 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.24), residues: 1248 helix: 2.29 (0.17), residues: 846 sheet: -1.53 (0.75), residues: 46 loop : -1.57 (0.32), residues: 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 161 time to evaluate : 1.190 Fit side-chains outliers start: 11 outliers final: 0 residues processed: 165 average time/residue: 0.1905 time to fit residues: 47.2463 Evaluate side-chains 161 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 30.0000 chunk 10 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10440 Z= 0.187 Angle : 0.534 7.688 14200 Z= 0.274 Chirality : 0.041 0.168 1604 Planarity : 0.004 0.053 1762 Dihedral : 4.178 24.124 1360 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.24), residues: 1248 helix: 2.33 (0.17), residues: 846 sheet: -1.64 (0.74), residues: 46 loop : -1.52 (0.33), residues: 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 162 time to evaluate : 1.994 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 163 average time/residue: 0.1863 time to fit residues: 45.7004 Evaluate side-chains 167 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 163 time to evaluate : 1.208 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0986 time to fit residues: 2.2342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 48 optimal weight: 0.0870 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 10440 Z= 0.172 Angle : 0.542 9.305 14200 Z= 0.273 Chirality : 0.042 0.245 1604 Planarity : 0.004 0.052 1762 Dihedral : 4.079 23.220 1360 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.24), residues: 1248 helix: 2.35 (0.17), residues: 846 sheet: -1.74 (0.74), residues: 46 loop : -1.59 (0.32), residues: 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 170 time to evaluate : 1.237 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 172 average time/residue: 0.1825 time to fit residues: 46.8797 Evaluate side-chains 171 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0941 time to fit residues: 2.2622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 10440 Z= 0.182 Angle : 0.543 9.931 14200 Z= 0.274 Chirality : 0.042 0.293 1604 Planarity : 0.004 0.052 1762 Dihedral : 4.076 23.094 1360 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.24), residues: 1248 helix: 2.34 (0.17), residues: 846 sheet: -1.80 (0.73), residues: 46 loop : -1.61 (0.32), residues: 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 175 time to evaluate : 1.249 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 177 average time/residue: 0.1810 time to fit residues: 48.1681 Evaluate side-chains 172 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.155 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10440 Z= 0.188 Angle : 0.556 10.581 14200 Z= 0.279 Chirality : 0.043 0.323 1604 Planarity : 0.004 0.052 1762 Dihedral : 4.072 22.676 1360 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.24), residues: 1248 helix: 2.30 (0.17), residues: 846 sheet: -1.83 (0.72), residues: 46 loop : -1.65 (0.32), residues: 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 173 time to evaluate : 1.159 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 175 average time/residue: 0.1859 time to fit residues: 48.5454 Evaluate side-chains 171 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.171 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 9.9990 chunk 56 optimal weight: 0.0170 chunk 83 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 10440 Z= 0.260 Angle : 0.605 11.270 14200 Z= 0.302 Chirality : 0.044 0.336 1604 Planarity : 0.005 0.052 1762 Dihedral : 4.217 22.474 1360 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.24), residues: 1248 helix: 2.24 (0.18), residues: 846 sheet: -1.91 (0.69), residues: 46 loop : -1.84 (0.32), residues: 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.256 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1865 time to fit residues: 47.2260 Evaluate side-chains 166 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.171 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.159069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.128557 restraints weight = 11761.803| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.46 r_work: 0.3201 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10440 Z= 0.186 Angle : 0.560 10.979 14200 Z= 0.282 Chirality : 0.043 0.322 1604 Planarity : 0.004 0.052 1762 Dihedral : 4.087 21.998 1360 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.24), residues: 1248 helix: 2.21 (0.17), residues: 858 sheet: -1.90 (0.70), residues: 46 loop : -1.96 (0.32), residues: 344 =============================================================================== Job complete usr+sys time: 2102.61 seconds wall clock time: 38 minutes 58.13 seconds (2338.13 seconds total)