Starting phenix.real_space_refine on Tue May 7 10:43:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r34_18860/05_2024/8r34_18860_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r34_18860/05_2024/8r34_18860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r34_18860/05_2024/8r34_18860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r34_18860/05_2024/8r34_18860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r34_18860/05_2024/8r34_18860_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r34_18860/05_2024/8r34_18860_updated.pdb" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.075 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 S 52 5.16 5 Na 4 4.78 5 C 5174 2.51 5 N 1136 2.21 5 O 1386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 381": "OD1" <-> "OD2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 572": "OD1" <-> "OD2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A GLU 755": "OE1" <-> "OE2" Residue "A ASP 835": "OD1" <-> "OD2" Residue "A PHE 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 381": "OD1" <-> "OD2" Residue "B PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 455": "OE1" <-> "OE2" Residue "B ASP 480": "OD1" <-> "OD2" Residue "B GLU 492": "OE1" <-> "OE2" Residue "B PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 572": "OD1" <-> "OD2" Residue "B GLU 755": "OE1" <-> "OE2" Residue "B ASP 757": "OD1" <-> "OD2" Residue "B ASP 795": "OD1" <-> "OD2" Residue "B PHE 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 7762 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3651 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 20, 'TRANS': 464} Chain breaks: 1 Chain: "B" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3651 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 20, 'TRANS': 464} Chain breaks: 1 Chain: "A" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 199 Unusual residues: {' NA': 2, '3PH': 4, 'PO4': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 199 Unusual residues: {' NA': 2, '3PH': 4, 'PO4': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Time building chain proxies: 4.92, per 1000 atoms: 0.63 Number of scatterers: 7762 At special positions: 0 Unit cell: (93.725, 93.725, 74.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 52 16.00 P 10 15.00 Na 4 11.00 O 1386 8.00 N 1136 7.00 C 5174 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: 3.30 Conformation dependent library (CDL) restraints added in 1.3 seconds 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1792 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 0 sheets defined 70.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 412 through 429 Processing helix chain 'A' and resid 436 through 454 removed outlier: 3.592A pdb=" N ALA A 443 " --> pdb=" O HIS A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 472 Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'A' and resid 500 through 517 Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.739A pdb=" N TRP A 527 " --> pdb=" O VAL A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 554 removed outlier: 3.751A pdb=" N TRP A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 568 through 571 No H-bonds generated for 'chain 'A' and resid 568 through 571' Processing helix chain 'A' and resid 579 through 597 removed outlier: 4.413A pdb=" N MET A 597 " --> pdb=" O ASN A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 616 Proline residue: A 615 - end of helix Processing helix chain 'A' and resid 620 through 645 removed outlier: 3.509A pdb=" N VAL A 626 " --> pdb=" O GLN A 622 " (cutoff:3.500A) Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 665 through 682 Processing helix chain 'A' and resid 684 through 686 No H-bonds generated for 'chain 'A' and resid 684 through 686' Processing helix chain 'A' and resid 688 through 691 No H-bonds generated for 'chain 'A' and resid 688 through 691' Processing helix chain 'A' and resid 694 through 706 removed outlier: 3.645A pdb=" N ILE A 699 " --> pdb=" O GLY A 695 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 700 " --> pdb=" O GLN A 696 " (cutoff:3.500A) Proline residue: A 701 - end of helix Processing helix chain 'A' and resid 713 through 717 Processing helix chain 'A' and resid 721 through 740 Processing helix chain 'A' and resid 742 through 754 removed outlier: 3.804A pdb=" N LYS A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 774 Processing helix chain 'A' and resid 779 through 795 Proline residue: A 788 - end of helix Processing helix chain 'A' and resid 802 through 815 removed outlier: 4.406A pdb=" N SER A 815 " --> pdb=" O ALA A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 831 Processing helix chain 'A' and resid 844 through 851 Processing helix chain 'A' and resid 853 through 873 removed outlier: 3.919A pdb=" N VAL A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER A 872 " --> pdb=" O GLY A 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 412 through 429 Processing helix chain 'B' and resid 436 through 454 removed outlier: 3.592A pdb=" N ALA B 443 " --> pdb=" O HIS B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 472 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 486 through 495 Processing helix chain 'B' and resid 500 through 517 Processing helix chain 'B' and resid 520 through 532 removed outlier: 3.523A pdb=" N SER B 526 " --> pdb=" O LYS B 522 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP B 527 " --> pdb=" O VAL B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 554 removed outlier: 3.749A pdb=" N TRP B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 Proline residue: B 569 - end of helix Processing helix chain 'B' and resid 579 through 597 removed outlier: 4.443A pdb=" N MET B 597 " --> pdb=" O ASN B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 616 Proline residue: B 615 - end of helix Processing helix chain 'B' and resid 620 through 645 Proline residue: B 629 - end of helix Processing helix chain 'B' and resid 665 through 682 Processing helix chain 'B' and resid 684 through 686 No H-bonds generated for 'chain 'B' and resid 684 through 686' Processing helix chain 'B' and resid 694 through 706 removed outlier: 3.656A pdb=" N ILE B 699 " --> pdb=" O GLY B 695 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE B 700 " --> pdb=" O GLN B 696 " (cutoff:3.500A) Proline residue: B 701 - end of helix Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 721 through 740 Processing helix chain 'B' and resid 742 through 754 removed outlier: 3.754A pdb=" N LYS B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 774 Processing helix chain 'B' and resid 779 through 795 Proline residue: B 788 - end of helix Processing helix chain 'B' and resid 802 through 815 removed outlier: 4.435A pdb=" N SER B 815 " --> pdb=" O ALA B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 831 Processing helix chain 'B' and resid 844 through 851 Processing helix chain 'B' and resid 853 through 873 removed outlier: 3.881A pdb=" N VAL B 862 " --> pdb=" O ALA B 858 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR B 867 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER B 872 " --> pdb=" O GLY B 868 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1296 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: 2.37 Time building geometry restraints manager: 3.42 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: 1168 1.33 - 1.45: 1899 1.45 - 1.57: 4685 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 7846 Sorted by residual: bond pdb=" O3 PO4 B 902 " pdb=" P PO4 B 902 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.46e+00 bond pdb=" O3 PO4 A 901 " pdb=" P PO4 A 901 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.41e+00 bond pdb=" O4 PO4 B 902 " pdb=" P PO4 B 902 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" O4 PO4 A 901 " pdb=" P PO4 A 901 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.62e+00 bond pdb=" O2 PO4 A 901 " pdb=" P PO4 A 901 " ideal model delta sigma weight residual 1.567 1.509 0.058 2.00e-02 2.50e+03 8.39e+00 ... (remaining 7841 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.25: 221 106.25 - 113.19: 4358 113.19 - 120.13: 2927 120.13 - 127.07: 2988 127.07 - 134.01: 80 Bond angle restraints: 10574 Sorted by residual: angle pdb=" C PHE A 656 " pdb=" N LYS A 657 " pdb=" CA LYS A 657 " ideal model delta sigma weight residual 121.61 127.22 -5.61 1.39e+00 5.18e-01 1.63e+01 angle pdb=" C ILE A 786 " pdb=" N ILE A 787 " pdb=" CA ILE A 787 " ideal model delta sigma weight residual 120.24 122.76 -2.52 6.30e-01 2.52e+00 1.60e+01 angle pdb=" C ILE B 786 " pdb=" N ILE B 787 " pdb=" CA ILE B 787 " ideal model delta sigma weight residual 120.24 122.54 -2.30 6.30e-01 2.52e+00 1.34e+01 angle pdb=" C ILE A 699 " pdb=" N ILE A 700 " pdb=" CA ILE A 700 " ideal model delta sigma weight residual 120.33 123.20 -2.87 8.00e-01 1.56e+00 1.29e+01 angle pdb=" C ILE B 699 " pdb=" N ILE B 700 " pdb=" CA ILE B 700 " ideal model delta sigma weight residual 120.33 123.07 -2.74 8.00e-01 1.56e+00 1.17e+01 ... (remaining 10569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 3923 17.40 - 34.80: 543 34.80 - 52.19: 193 52.19 - 69.59: 78 69.59 - 86.99: 11 Dihedral angle restraints: 4748 sinusoidal: 1966 harmonic: 2782 Sorted by residual: dihedral pdb=" CA GLU A 755 " pdb=" C GLU A 755 " pdb=" N ASN A 756 " pdb=" CA ASN A 756 " ideal model delta harmonic sigma weight residual 180.00 -161.14 -18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CG ARG A 850 " pdb=" CD ARG A 850 " pdb=" NE ARG A 850 " pdb=" CZ ARG A 850 " ideal model delta sinusoidal sigma weight residual 180.00 -136.60 -43.40 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CA LYS A 735 " pdb=" CB LYS A 735 " pdb=" CG LYS A 735 " pdb=" CD LYS A 735 " ideal model delta sinusoidal sigma weight residual -180.00 -120.22 -59.78 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 786 0.033 - 0.066: 357 0.066 - 0.099: 97 0.099 - 0.132: 20 0.132 - 0.164: 2 Chirality restraints: 1262 Sorted by residual: chirality pdb=" CG LEU A 408 " pdb=" CB LEU A 408 " pdb=" CD1 LEU A 408 " pdb=" CD2 LEU A 408 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CG LEU B 408 " pdb=" CB LEU B 408 " pdb=" CD1 LEU B 408 " pdb=" CD2 LEU B 408 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ASN A 756 " pdb=" N ASN A 756 " pdb=" C ASN A 756 " pdb=" CB ASN A 756 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1259 not shown) Planarity restraints: 1226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 719 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.15e+00 pdb=" N PRO B 720 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 720 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 720 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 643 " 0.013 2.00e-02 2.50e+03 1.29e-02 2.91e+00 pdb=" CG PHE B 643 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE B 643 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 643 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 643 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 643 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 643 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 719 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO A 720 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 720 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 720 " -0.023 5.00e-02 4.00e+02 ... (remaining 1223 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 264 2.71 - 3.26: 7771 3.26 - 3.81: 12830 3.81 - 4.35: 17715 4.35 - 4.90: 28605 Nonbonded interactions: 67185 Sorted by model distance: nonbonded pdb=" O LEU B 860 " pdb=" OG1 THR B 864 " model vdw 2.167 2.440 nonbonded pdb=" O LEU A 860 " pdb=" OG1 THR A 864 " model vdw 2.202 2.440 nonbonded pdb=" O ILE B 601 " pdb=" O HOH B1001 " model vdw 2.223 2.440 nonbonded pdb=" O ILE A 601 " pdb=" O HOH A1001 " model vdw 2.227 2.440 nonbonded pdb=" O MET A 648 " pdb=" OG1 THR A 651 " model vdw 2.244 2.440 ... (remaining 67180 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' and (resid 378 through 876 or resid 903 or resid 905 through 907)) selection = (chain 'B' and (resid 378 through 876 or resid 903 or resid 905 through 907)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.320 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: 10.110 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.650 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:14.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.004 0.062 7846 Z= 0.266 Angle : 0.647 5.608 10574 Z= 0.392 Chirality : 0.040 0.164 1262 Planarity : 0.005 0.044 1226 Dihedral : 19.662 86.987 2956 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.41 % Allowed : 24.94 % Favored : 72.66 % 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: 0.34 (0.27), residues: 962 helix: 0.71 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -0.99 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 639 HIS 0.004 0.001 HIS B 439 PHE 0.030 0.002 PHE B 643 TYR 0.013 0.001 TYR B 841 ARG 0.001 0.000 ARG A 836 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 0.812 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 105 average time/residue: 1.2426 time to fit residues: 138.4161 Evaluate side-chains 102 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.8086 moved from start: 0.0581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7846 Z= 0.278 Angle : 0.563 5.809 10574 Z= 0.282 Chirality : 0.041 0.144 1262 Planarity : 0.005 0.042 1226 Dihedral : 16.617 84.461 1377 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.68 % Allowed : 22.03 % Favored : 73.29 % 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: 0.57 (0.27), residues: 962 helix: 0.82 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -0.73 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 639 HIS 0.004 0.002 HIS B 439 PHE 0.031 0.002 PHE B 643 TYR 0.011 0.001 TYR B 841 ARG 0.001 0.000 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 90 time to evaluate : 0.823 Fit side-chains REVERT: A 431 LYS cc_start: 0.6931 (OUTLIER) cc_final: 0.5941 (tptt) REVERT: B 537 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6732 (ptp-170) REVERT: B 735 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7050 (tttm) REVERT: B 801 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6864 (mttt) REVERT: B 850 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7041 (mpt180) outliers start: 37 outliers final: 16 residues processed: 112 average time/residue: 1.2474 time to fit residues: 148.3236 Evaluate side-chains 109 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 735 LYS Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 850 ARG Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.8077 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7846 Z= 0.239 Angle : 0.532 5.446 10574 Z= 0.265 Chirality : 0.040 0.137 1262 Planarity : 0.005 0.041 1226 Dihedral : 16.215 81.004 1370 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.18 % Allowed : 22.78 % Favored : 73.04 % 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: 0.90 (0.27), residues: 962 helix: 1.08 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -0.67 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 639 HIS 0.004 0.002 HIS B 439 PHE 0.028 0.002 PHE B 643 TYR 0.010 0.001 TYR B 841 ARG 0.001 0.000 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 86 time to evaluate : 0.822 Fit side-chains REVERT: A 431 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.5950 (tptt) REVERT: B 537 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.6725 (ptp-170) REVERT: B 801 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6815 (mttt) REVERT: B 850 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7006 (mpt180) REVERT: B 875 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7151 (mmmt) outliers start: 33 outliers final: 15 residues processed: 104 average time/residue: 1.2907 time to fit residues: 142.1000 Evaluate side-chains 105 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 850 ARG Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.3980 chunk 65 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 92 optimal weight: 0.0870 chunk 83 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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: 0.8051 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7846 Z= 0.171 Angle : 0.486 5.319 10574 Z= 0.241 Chirality : 0.038 0.128 1262 Planarity : 0.004 0.037 1226 Dihedral : 15.603 83.467 1368 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.67 % Allowed : 22.66 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.27), residues: 962 helix: 1.41 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -0.59 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 639 HIS 0.003 0.001 HIS B 439 PHE 0.025 0.001 PHE B 643 TYR 0.007 0.001 TYR B 841 ARG 0.001 0.000 ARG A 836 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 88 time to evaluate : 0.922 Fit side-chains REVERT: A 431 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.5924 (tptt) REVERT: B 537 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6707 (ptp-170) REVERT: B 850 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7135 (mpt180) outliers start: 29 outliers final: 10 residues processed: 103 average time/residue: 1.2537 time to fit residues: 136.9408 Evaluate side-chains 99 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 850 ARG Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 0 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.8060 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7846 Z= 0.194 Angle : 0.500 5.354 10574 Z= 0.247 Chirality : 0.039 0.131 1262 Planarity : 0.004 0.036 1226 Dihedral : 14.921 86.126 1360 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.80 % Allowed : 22.66 % Favored : 73.54 % 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: 1.36 (0.27), residues: 962 helix: 1.43 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -0.59 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 639 HIS 0.003 0.001 HIS B 439 PHE 0.025 0.001 PHE A 643 TYR 0.008 0.001 TYR B 841 ARG 0.001 0.000 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 85 time to evaluate : 0.934 Fit side-chains REVERT: A 431 LYS cc_start: 0.6951 (OUTLIER) cc_final: 0.5968 (tptt) REVERT: B 537 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6692 (ptp-170) REVERT: B 850 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.6978 (mpt180) REVERT: B 875 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7472 (mmmt) outliers start: 30 outliers final: 14 residues processed: 98 average time/residue: 1.2241 time to fit residues: 127.5707 Evaluate side-chains 102 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 850 ARG Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.6980 chunk 18 optimal weight: 0.0370 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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: 0.8049 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7846 Z= 0.176 Angle : 0.490 5.317 10574 Z= 0.241 Chirality : 0.038 0.136 1262 Planarity : 0.004 0.035 1226 Dihedral : 14.416 89.065 1360 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.42 % Allowed : 23.54 % Favored : 73.04 % 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: 1.51 (0.27), residues: 962 helix: 1.56 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -0.57 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 639 HIS 0.003 0.001 HIS B 439 PHE 0.025 0.001 PHE B 643 TYR 0.007 0.001 TYR B 841 ARG 0.001 0.000 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 86 time to evaluate : 0.912 Fit side-chains REVERT: A 431 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.5932 (tptt) REVERT: A 875 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7447 (mmmt) REVERT: B 537 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.6675 (ptp-170) REVERT: B 850 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7136 (mpt180) outliers start: 27 outliers final: 15 residues processed: 100 average time/residue: 1.2062 time to fit residues: 128.5500 Evaluate side-chains 103 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 850 ARG Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 92 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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: 0.8051 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7846 Z= 0.182 Angle : 0.494 5.327 10574 Z= 0.243 Chirality : 0.039 0.132 1262 Planarity : 0.004 0.034 1226 Dihedral : 14.042 87.990 1360 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.78 % Allowed : 24.30 % Favored : 72.91 % 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 (0.27), residues: 962 helix: 1.55 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -0.51 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 639 HIS 0.003 0.001 HIS B 439 PHE 0.025 0.001 PHE B 643 TYR 0.007 0.001 TYR B 841 ARG 0.001 0.000 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 1.101 Fit side-chains REVERT: A 431 LYS cc_start: 0.6972 (OUTLIER) cc_final: 0.5949 (tptt) REVERT: B 850 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7134 (mpt180) REVERT: B 875 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7460 (mmmt) outliers start: 22 outliers final: 14 residues processed: 96 average time/residue: 1.4056 time to fit residues: 142.9394 Evaluate side-chains 101 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 850 ARG Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 58 optimal weight: 0.0870 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 72 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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: 0.8019 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7846 Z= 0.136 Angle : 0.462 5.274 10574 Z= 0.226 Chirality : 0.037 0.128 1262 Planarity : 0.004 0.032 1226 Dihedral : 13.402 83.524 1360 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.15 % Allowed : 25.06 % Favored : 72.78 % 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: 1.80 (0.27), residues: 962 helix: 1.78 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -0.52 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 639 HIS 0.002 0.001 HIS B 439 PHE 0.021 0.001 PHE B 643 TYR 0.005 0.001 TYR A 518 ARG 0.001 0.000 ARG A 836 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.873 Fit side-chains REVERT: A 431 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.5958 (tptt) REVERT: A 875 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7438 (mmmt) REVERT: B 875 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7467 (mmmt) outliers start: 17 outliers final: 6 residues processed: 97 average time/residue: 1.2727 time to fit residues: 130.9515 Evaluate side-chains 94 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.0570 chunk 77 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 0.0970 chunk 91 optimal weight: 0.6980 overall best weight: 0.5296 ------------------------------------------------------------------------------- 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: 0.8030 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7846 Z= 0.153 Angle : 0.471 5.308 10574 Z= 0.232 Chirality : 0.038 0.126 1262 Planarity : 0.004 0.032 1226 Dihedral : 13.195 83.604 1356 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.77 % Allowed : 25.19 % Favored : 73.04 % 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: 1.79 (0.27), residues: 962 helix: 1.77 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -0.51 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 639 HIS 0.003 0.001 HIS B 439 PHE 0.023 0.001 PHE B 643 TYR 0.006 0.001 TYR B 841 ARG 0.008 0.000 ARG B 836 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.815 Fit side-chains REVERT: A 431 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.5974 (tptt) REVERT: A 875 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7440 (mmmt) REVERT: B 624 PHE cc_start: 0.7982 (m-80) cc_final: 0.7761 (m-80) REVERT: B 875 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7463 (mmmt) outliers start: 14 outliers final: 8 residues processed: 90 average time/residue: 1.3502 time to fit residues: 128.4919 Evaluate side-chains 92 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8048 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7846 Z= 0.187 Angle : 0.498 5.331 10574 Z= 0.245 Chirality : 0.039 0.131 1262 Planarity : 0.004 0.034 1226 Dihedral : 13.339 85.005 1356 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.52 % Allowed : 25.57 % Favored : 72.91 % 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: 1.67 (0.27), residues: 962 helix: 1.66 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -0.47 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 639 HIS 0.003 0.001 HIS B 439 PHE 0.026 0.001 PHE B 643 TYR 0.007 0.001 TYR B 841 ARG 0.007 0.001 ARG B 836 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.816 Fit side-chains REVERT: A 431 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.5971 (tptt) REVERT: A 875 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7432 (mmmt) REVERT: B 875 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7476 (mmmt) outliers start: 12 outliers final: 7 residues processed: 87 average time/residue: 1.3651 time to fit residues: 125.3939 Evaluate side-chains 88 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.0470 chunk 66 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 overall best weight: 0.8682 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.144919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119560 restraints weight = 7893.867| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.41 r_work: 0.3356 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7846 Z= 0.200 Angle : 0.506 5.358 10574 Z= 0.249 Chirality : 0.039 0.133 1262 Planarity : 0.004 0.034 1226 Dihedral : 13.390 87.529 1356 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.52 % Allowed : 25.70 % Favored : 72.78 % 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: 1.58 (0.27), residues: 962 helix: 1.58 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -0.46 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 639 HIS 0.003 0.001 HIS B 439 PHE 0.026 0.001 PHE B 643 TYR 0.007 0.001 TYR B 841 ARG 0.007 0.001 ARG B 836 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3022.31 seconds wall clock time: 56 minutes 34.50 seconds (3394.50 seconds total)