Starting phenix.real_space_refine on Tue Feb 11 04:46:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wr7_32717/02_2025/7wr7_32717.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wr7_32717/02_2025/7wr7_32717.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/cci-nas-00/data/ceres_data/7wr7_32717/02_2025/7wr7_32717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wr7_32717/02_2025/7wr7_32717.map" model { file = "/net/cci-nas-00/data/ceres_data/7wr7_32717/02_2025/7wr7_32717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wr7_32717/02_2025/7wr7_32717.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 34 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 2509 2.51 5 N 681 2.21 5 O 776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3995 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2013 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 15, 'TRANS': 245} Chain: "B" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1844 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 220} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 68 Unusual residues: {'GBS': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GBS:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.37, per 1000 atoms: 0.84 Number of scatterers: 3995 At special positions: 0 Unit cell: (64.852, 80.542, 95.186, 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 29 16.00 O 776 8.00 N 681 7.00 C 2509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 677 " distance=2.03 Simple disulfide: pdb=" SG CYS A 716 " - pdb=" SG CYS A 767 " distance=2.03 Simple disulfide: pdb=" SG CYS A 772 " - pdb=" SG CYS B 896 " distance=2.03 Simple disulfide: pdb=" SG CYS B 810 " - pdb=" SG CYS B 826 " distance=2.03 Simple disulfide: pdb=" SG CYS B 910 " - pdb=" SG CYS B 977 " distance=2.03 Simple disulfide: pdb=" SG CYS B 941 " - pdb=" SG CYS B 956 " distance=2.03 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS B 995 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 534 " " NAG A 802 " - " ASN A 630 " " NAG A 803 " - " ASN A 682 " " NAG A 804 " - " ASN A 706 " " NAG A 805 " - " ASN A 725 " " NAG B1101 " - " ASN B 848 " " NAG B1102 " - " ASN B 887 " " NAG B1103 " - " ASN B 909 " " NAG B1104 " - " ASN B 949 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 466.3 milliseconds 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 904 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 7 sheets defined 7.9% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 671 through 675 Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'B' and resid 833 through 835 No H-bonds generated for 'chain 'B' and resid 833 through 835' Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 1010 through 1019 removed outlier: 4.071A pdb=" N PHE B1017 " --> pdb=" O TRP B1013 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS B1019 " --> pdb=" O GLN B1015 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 538 removed outlier: 3.744A pdb=" N PHE A 537 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 629 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 572 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN A 630 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N PHE A 568 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR A 632 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU A 566 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY A 634 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE A 564 " --> pdb=" O GLY A 634 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 551 through 557 removed outlier: 3.757A pdb=" N CYS A 552 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 594 " --> pdb=" O ILE A 582 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 693 through 694 Processing sheet with id=AA4, first strand: chain 'A' and resid 728 through 729 removed outlier: 3.899A pdb=" N LYS A 728 " --> pdb=" O ARG A 764 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 740 through 741 removed outlier: 3.705A pdb=" N THR A 752 " --> pdb=" O LYS A 740 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 789 through 790 removed outlier: 3.856A pdb=" N GLN B 929 " --> pdb=" O GLY B 914 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 914 " --> pdb=" O GLN B 929 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ASN B 909 " --> pdb=" O GLN B 978 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLN B 978 " --> pdb=" O ASN B 909 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA B 913 " --> pdb=" O PRO B 974 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU B 975 " --> pdb=" O ALA B 986 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS B 977 " --> pdb=" O PHE B 984 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL B1003 " --> pdb=" O SER B 990 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 820 through 821 removed outlier: 5.813A pdb=" N LEU B 808 " --> pdb=" O TYR B 804 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR B 804 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N CYS B 810 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 802 " --> pdb=" O CYS B 810 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N TRP B 837 " --> pdb=" O ILE B 859 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU B 861 " --> pdb=" O HIS B 881 " (cutoff:3.500A) 77 hydrogen bonds defined for protein. 198 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.99 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1015 1.33 - 1.45: 823 1.45 - 1.57: 2218 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 4092 Sorted by residual: bond pdb=" C18 GBS B1105 " pdb=" N3 GBS B1105 " ideal model delta sigma weight residual 1.387 1.333 0.054 2.00e-02 2.50e+03 7.17e+00 bond pdb=" N GLN B 968 " pdb=" CA GLN B 968 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.25e-02 6.40e+03 6.52e+00 bond pdb=" O GBS B1105 " pdb=" C6 GBS B1105 " ideal model delta sigma weight residual 1.260 1.210 0.050 2.00e-02 2.50e+03 6.17e+00 bond pdb=" N SER B 971 " pdb=" CA SER B 971 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.23e-02 6.61e+03 6.15e+00 bond pdb=" N GLY B 973 " pdb=" CA GLY B 973 " ideal model delta sigma weight residual 1.443 1.476 -0.033 1.37e-02 5.33e+03 5.83e+00 ... (remaining 4087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 5343 1.40 - 2.81: 185 2.81 - 4.21: 31 4.21 - 5.62: 5 5.62 - 7.02: 5 Bond angle restraints: 5569 Sorted by residual: angle pdb=" N ASP B 970 " pdb=" CA ASP B 970 " pdb=" C ASP B 970 " ideal model delta sigma weight residual 114.56 108.41 6.15 1.27e+00 6.20e-01 2.35e+01 angle pdb=" N PRO B 974 " pdb=" CA PRO B 974 " pdb=" CB PRO B 974 " ideal model delta sigma weight residual 103.25 98.83 4.42 1.05e+00 9.07e-01 1.77e+01 angle pdb=" CA GLN B 968 " pdb=" C GLN B 968 " pdb=" O GLN B 968 " ideal model delta sigma weight residual 121.55 118.32 3.23 1.06e+00 8.90e-01 9.31e+00 angle pdb=" N GLY B 972 " pdb=" CA GLY B 972 " pdb=" C GLY B 972 " ideal model delta sigma weight residual 115.32 111.24 4.08 1.38e+00 5.25e-01 8.75e+00 angle pdb=" N PHE A 542 " pdb=" CA PHE A 542 " pdb=" C PHE A 542 " ideal model delta sigma weight residual 109.81 115.70 -5.89 2.21e+00 2.05e-01 7.10e+00 ... (remaining 5564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.22: 2391 16.22 - 32.45: 115 32.45 - 48.67: 30 48.67 - 64.89: 9 64.89 - 81.12: 1 Dihedral angle restraints: 2546 sinusoidal: 1134 harmonic: 1412 Sorted by residual: dihedral pdb=" CA PRO A 543 " pdb=" C PRO A 543 " pdb=" N ASN A 544 " pdb=" CA ASN A 544 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CB CYS A 772 " pdb=" SG CYS A 772 " pdb=" SG CYS B 896 " pdb=" CB CYS B 896 " ideal model delta sinusoidal sigma weight residual -86.00 -113.70 27.70 1 1.00e+01 1.00e-02 1.10e+01 dihedral pdb=" CA SER A 539 " pdb=" C SER A 539 " pdb=" N THR A 540 " pdb=" CA THR A 540 " ideal model delta harmonic sigma weight residual 180.00 163.44 16.56 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 2543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 404 0.033 - 0.067: 140 0.067 - 0.100: 55 0.100 - 0.134: 28 0.134 - 0.167: 1 Chirality restraints: 628 Sorted by residual: chirality pdb=" C2 NAG A 804 " pdb=" C1 NAG A 804 " pdb=" C3 NAG A 804 " pdb=" N2 NAG A 804 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA VAL B 988 " pdb=" N VAL B 988 " pdb=" C VAL B 988 " pdb=" CB VAL B 988 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CB VAL A 691 " pdb=" CA VAL A 691 " pdb=" CG1 VAL A 691 " pdb=" CG2 VAL A 691 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 625 not shown) Planarity restraints: 733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 GBS B1105 " 0.013 2.00e-02 2.50e+03 3.50e-02 1.53e+01 pdb=" C2 GBS B1105 " -0.041 2.00e-02 2.50e+03 pdb=" N2 GBS B1105 " 0.055 2.00e-02 2.50e+03 pdb=" N3 GBS B1105 " -0.034 2.00e-02 2.50e+03 pdb=" N4 GBS B1105 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GBS B1105 " -0.026 2.00e-02 2.50e+03 2.49e-02 1.24e+01 pdb=" C1 GBS B1105 " 0.009 2.00e-02 2.50e+03 pdb=" C2 GBS B1105 " 0.028 2.00e-02 2.50e+03 pdb=" C3 GBS B1105 " 0.008 2.00e-02 2.50e+03 pdb=" C4 GBS B1105 " -0.026 2.00e-02 2.50e+03 pdb=" C5 GBS B1105 " -0.031 2.00e-02 2.50e+03 pdb=" C6 GBS B1105 " 0.041 2.00e-02 2.50e+03 pdb=" N2 GBS B1105 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 532 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO A 533 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 533 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 533 " -0.022 5.00e-02 4.00e+02 ... (remaining 730 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1243 2.83 - 3.35: 3694 3.35 - 3.86: 6398 3.86 - 4.38: 7329 4.38 - 4.90: 12603 Nonbonded interactions: 31267 Sorted by model distance: nonbonded pdb=" OD2 ASP B 874 " pdb=" ND2 ASN B 875 " model vdw 2.309 3.120 nonbonded pdb=" NH2 ARG B 908 " pdb=" O GLN B 978 " model vdw 2.350 3.120 nonbonded pdb=" O GLY B 811 " pdb=" O GLY B 972 " model vdw 2.357 3.040 nonbonded pdb=" NZ LYS A 740 " pdb=" O SER A 754 " model vdw 2.359 3.120 nonbonded pdb=" O CYS B 826 " pdb=" NH1 ARG B 830 " model vdw 2.367 3.120 ... (remaining 31262 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.030 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 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 0.054 4092 Z= 0.219 Angle : 0.607 7.023 5569 Z= 0.331 Chirality : 0.044 0.167 628 Planarity : 0.003 0.039 724 Dihedral : 10.283 81.116 1618 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 3.29 % Allowed : 6.59 % Favored : 90.12 % 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: -4.53 (0.30), residues: 492 helix: -2.64 (0.51), residues: 36 sheet: -2.64 (0.42), residues: 105 loop : -3.42 (0.28), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 699 HIS 0.002 0.000 HIS B 825 PHE 0.005 0.001 PHE A 627 TYR 0.004 0.001 TYR A 546 ARG 0.001 0.000 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 ARG cc_start: 0.8346 (ptp-170) cc_final: 0.7770 (mtm110) REVERT: A 707 TRP cc_start: 0.8525 (t-100) cc_final: 0.7932 (t-100) REVERT: B 959 TYR cc_start: 0.8034 (m-80) cc_final: 0.7809 (m-10) outliers start: 14 outliers final: 5 residues processed: 121 average time/residue: 0.2292 time to fit residues: 32.3125 Evaluate side-chains 77 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 660 ASN Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 896 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 20 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 649 GLN A 713 ASN A 717 GLN ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 GLN B 938 ASN B 943 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.168900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.119326 restraints weight = 5064.340| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.36 r_work: 0.3605 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4092 Z= 0.250 Angle : 0.614 9.545 5569 Z= 0.310 Chirality : 0.047 0.245 628 Planarity : 0.004 0.045 724 Dihedral : 7.568 55.607 728 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 3.06 % Allowed : 13.41 % Favored : 83.53 % 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: -3.88 (0.34), residues: 492 helix: -1.94 (0.69), residues: 38 sheet: -2.30 (0.38), residues: 127 loop : -2.94 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1013 HIS 0.004 0.001 HIS A 665 PHE 0.010 0.001 PHE A 542 TYR 0.007 0.001 TYR B 920 ARG 0.004 0.001 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 707 TRP cc_start: 0.8689 (t-100) cc_final: 0.8001 (t-100) REVERT: B 803 TYR cc_start: 0.8457 (m-80) cc_final: 0.7865 (m-80) REVERT: B 859 ILE cc_start: 0.8313 (mm) cc_final: 0.7930 (mm) REVERT: B 954 MET cc_start: 0.7419 (mtt) cc_final: 0.7184 (mtm) REVERT: B 1017 PHE cc_start: 0.7518 (m-10) cc_final: 0.7244 (m-10) outliers start: 13 outliers final: 6 residues processed: 80 average time/residue: 0.2217 time to fit residues: 21.0517 Evaluate side-chains 73 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 911 SER Chi-restraints excluded: chain B residue 938 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 13 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 47 optimal weight: 0.0870 chunk 11 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 ASN B 844 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.178537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.128893 restraints weight = 5203.189| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 3.69 r_work: 0.3601 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4092 Z= 0.202 Angle : 0.574 9.432 5569 Z= 0.287 Chirality : 0.046 0.242 628 Planarity : 0.004 0.054 724 Dihedral : 6.944 55.967 721 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 2.35 % Allowed : 14.35 % Favored : 83.29 % 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: -3.51 (0.34), residues: 492 helix: -1.41 (0.75), residues: 38 sheet: -1.80 (0.40), residues: 117 loop : -2.83 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 798 HIS 0.005 0.001 HIS A 665 PHE 0.008 0.001 PHE A 627 TYR 0.007 0.001 TYR B 920 ARG 0.003 0.001 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 540 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7805 (p) REVERT: A 565 GLN cc_start: 0.8334 (tt0) cc_final: 0.7870 (tt0) REVERT: A 679 ARG cc_start: 0.8722 (ptp-170) cc_final: 0.8227 (mtm110) REVERT: A 717 GLN cc_start: 0.8851 (pp30) cc_final: 0.8642 (pp30) REVERT: A 766 GLN cc_start: 0.7288 (mm-40) cc_final: 0.6991 (mm-40) REVERT: B 803 TYR cc_start: 0.8454 (m-80) cc_final: 0.7771 (m-80) REVERT: B 859 ILE cc_start: 0.8323 (mm) cc_final: 0.7969 (mm) outliers start: 10 outliers final: 7 residues processed: 75 average time/residue: 0.1734 time to fit residues: 16.1609 Evaluate side-chains 69 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 660 ASN Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN A 660 ASN B 938 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.174408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.124289 restraints weight = 5266.647| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 3.61 r_work: 0.3510 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4092 Z= 0.308 Angle : 0.611 9.330 5569 Z= 0.312 Chirality : 0.047 0.234 628 Planarity : 0.004 0.047 724 Dihedral : 7.031 56.012 721 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 2.82 % Allowed : 14.82 % Favored : 82.35 % 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: -3.41 (0.35), residues: 492 helix: -1.05 (0.80), residues: 38 sheet: -2.00 (0.39), residues: 138 loop : -2.68 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 798 HIS 0.004 0.001 HIS A 567 PHE 0.010 0.001 PHE A 627 TYR 0.008 0.001 TYR B1004 ARG 0.005 0.001 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 GLN cc_start: 0.8497 (tt0) cc_final: 0.8086 (tt0) REVERT: A 679 ARG cc_start: 0.8724 (ptp-170) cc_final: 0.8456 (ptp-170) REVERT: A 717 GLN cc_start: 0.8916 (pp30) cc_final: 0.8656 (pp30) REVERT: A 766 GLN cc_start: 0.7339 (mm-40) cc_final: 0.7051 (mm-40) REVERT: B 803 TYR cc_start: 0.8589 (m-80) cc_final: 0.7632 (m-80) REVERT: B 859 ILE cc_start: 0.8358 (mm) cc_final: 0.7998 (mm) outliers start: 12 outliers final: 8 residues processed: 71 average time/residue: 0.1918 time to fit residues: 16.9907 Evaluate side-chains 66 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 911 SER Chi-restraints excluded: chain B residue 938 ASN Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.167215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.117423 restraints weight = 5177.016| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.37 r_work: 0.3569 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4092 Z= 0.250 Angle : 0.588 9.377 5569 Z= 0.299 Chirality : 0.046 0.231 628 Planarity : 0.005 0.061 724 Dihedral : 6.887 56.639 720 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 2.82 % Allowed : 16.47 % Favored : 80.71 % 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: -3.29 (0.36), residues: 492 helix: -0.92 (0.81), residues: 38 sheet: -1.93 (0.39), residues: 143 loop : -2.60 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 798 HIS 0.003 0.001 HIS A 567 PHE 0.011 0.001 PHE A 542 TYR 0.008 0.001 TYR B 920 ARG 0.004 0.000 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7700 (tp) cc_final: 0.7229 (tt) REVERT: A 679 ARG cc_start: 0.8730 (ptp-170) cc_final: 0.8457 (ptp-170) REVERT: A 766 GLN cc_start: 0.7538 (mm-40) cc_final: 0.7182 (mm-40) REVERT: B 803 TYR cc_start: 0.8631 (m-80) cc_final: 0.7656 (m-80) REVERT: B 859 ILE cc_start: 0.8371 (mm) cc_final: 0.8018 (mm) outliers start: 12 outliers final: 9 residues processed: 69 average time/residue: 0.1763 time to fit residues: 15.0340 Evaluate side-chains 67 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 911 SER Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 18 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 ASN B 938 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.158464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.110051 restraints weight = 5315.226| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.43 r_work: 0.3509 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4092 Z= 0.248 Angle : 0.583 9.346 5569 Z= 0.296 Chirality : 0.046 0.230 628 Planarity : 0.004 0.047 724 Dihedral : 6.890 57.407 720 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 2.82 % Allowed : 16.94 % Favored : 80.24 % 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: -3.20 (0.36), residues: 492 helix: -0.78 (0.84), residues: 38 sheet: -1.92 (0.39), residues: 143 loop : -2.52 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 798 HIS 0.003 0.001 HIS A 567 PHE 0.014 0.001 PHE A 681 TYR 0.008 0.001 TYR B 920 ARG 0.007 0.001 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7668 (tp) cc_final: 0.7227 (tt) REVERT: A 679 ARG cc_start: 0.8698 (ptp-170) cc_final: 0.8425 (ptp-170) REVERT: A 707 TRP cc_start: 0.8605 (t-100) cc_final: 0.8354 (t-100) REVERT: A 766 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7273 (mm-40) REVERT: B 803 TYR cc_start: 0.8668 (m-80) cc_final: 0.7637 (m-80) REVERT: B 807 ARG cc_start: 0.7928 (mtp-110) cc_final: 0.7722 (mtp85) REVERT: B 859 ILE cc_start: 0.8343 (mm) cc_final: 0.7979 (mm) REVERT: B 993 TYR cc_start: 0.7897 (t80) cc_final: 0.7678 (t80) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.1678 time to fit residues: 13.9393 Evaluate side-chains 63 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.150553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.101942 restraints weight = 5393.375| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.58 r_work: 0.3280 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4092 Z= 0.261 Angle : 0.593 9.338 5569 Z= 0.301 Chirality : 0.046 0.227 628 Planarity : 0.005 0.068 724 Dihedral : 6.916 58.303 720 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 2.12 % Allowed : 17.88 % Favored : 80.00 % 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: -3.15 (0.36), residues: 492 helix: -0.79 (0.83), residues: 38 sheet: -1.92 (0.39), residues: 143 loop : -2.45 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 798 HIS 0.004 0.001 HIS A 567 PHE 0.017 0.002 PHE A 681 TYR 0.009 0.001 TYR B 920 ARG 0.006 0.001 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7716 (tp) cc_final: 0.7327 (tt) REVERT: A 679 ARG cc_start: 0.8660 (ptp-170) cc_final: 0.8138 (ptp-170) REVERT: A 707 TRP cc_start: 0.8568 (t-100) cc_final: 0.8274 (t-100) REVERT: A 766 GLN cc_start: 0.7756 (mm-40) cc_final: 0.7491 (mm-40) REVERT: B 803 TYR cc_start: 0.8743 (m-80) cc_final: 0.7667 (m-80) REVERT: B 859 ILE cc_start: 0.8395 (mm) cc_final: 0.8033 (mm) outliers start: 9 outliers final: 7 residues processed: 67 average time/residue: 0.1907 time to fit residues: 16.0018 Evaluate side-chains 64 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 GLN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.146552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.098128 restraints weight = 5407.266| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.58 r_work: 0.3258 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 4092 Z= 0.432 Angle : 0.682 9.189 5569 Z= 0.350 Chirality : 0.048 0.220 628 Planarity : 0.005 0.045 724 Dihedral : 7.281 59.562 720 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.82 % Favored : 86.18 % Rotamer: Outliers : 3.06 % Allowed : 17.18 % Favored : 79.76 % 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: -3.31 (0.37), residues: 492 helix: -0.80 (0.82), residues: 38 sheet: -2.26 (0.39), residues: 144 loop : -2.44 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 707 HIS 0.006 0.001 HIS A 567 PHE 0.019 0.002 PHE A 681 TYR 0.012 0.002 TYR B 920 ARG 0.004 0.001 ARG B 940 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7857 (tp) cc_final: 0.7555 (tt) REVERT: A 707 TRP cc_start: 0.8695 (t-100) cc_final: 0.8376 (t-100) REVERT: A 766 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7560 (mm-40) REVERT: B 803 TYR cc_start: 0.8853 (m-80) cc_final: 0.7690 (m-80) REVERT: B 896 CYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7656 (m) outliers start: 13 outliers final: 8 residues processed: 64 average time/residue: 0.1727 time to fit residues: 13.7587 Evaluate side-chains 62 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 938 ASN Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 12 optimal weight: 0.0270 chunk 2 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 0.0370 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.153076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.104834 restraints weight = 5300.562| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.59 r_work: 0.3318 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4092 Z= 0.169 Angle : 0.610 9.380 5569 Z= 0.311 Chirality : 0.046 0.226 628 Planarity : 0.005 0.053 724 Dihedral : 6.899 59.247 720 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 0.94 % Allowed : 20.00 % Favored : 79.06 % 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: -3.02 (0.37), residues: 492 helix: -0.86 (0.82), residues: 38 sheet: -1.97 (0.42), residues: 133 loop : -2.27 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 915 HIS 0.002 0.000 HIS A 567 PHE 0.012 0.001 PHE A 681 TYR 0.009 0.001 TYR B 920 ARG 0.009 0.001 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7630 (tp) cc_final: 0.7223 (tt) REVERT: A 707 TRP cc_start: 0.8542 (t-100) cc_final: 0.8258 (t-100) REVERT: A 717 GLN cc_start: 0.8976 (pp30) cc_final: 0.8684 (pp30) REVERT: A 766 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7545 (mm-40) REVERT: B 803 TYR cc_start: 0.8658 (m-80) cc_final: 0.7600 (m-80) REVERT: B 807 ARG cc_start: 0.7982 (mtp-110) cc_final: 0.7739 (ttp80) REVERT: B 859 ILE cc_start: 0.8333 (mm) cc_final: 0.7974 (mm) REVERT: B 896 CYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7317 (m) outliers start: 4 outliers final: 3 residues processed: 63 average time/residue: 0.1781 time to fit residues: 13.9832 Evaluate side-chains 63 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 896 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.149651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.101217 restraints weight = 5414.309| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.59 r_work: 0.3270 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4092 Z= 0.265 Angle : 0.620 9.306 5569 Z= 0.318 Chirality : 0.047 0.224 628 Planarity : 0.005 0.047 724 Dihedral : 6.915 59.712 720 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 1.41 % Allowed : 19.76 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.37), residues: 492 helix: -0.77 (0.84), residues: 38 sheet: -1.95 (0.40), residues: 145 loop : -2.21 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 699 HIS 0.004 0.001 HIS A 567 PHE 0.016 0.002 PHE A 681 TYR 0.010 0.001 TYR B 920 ARG 0.008 0.001 ARG B 807 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7907 (tp) cc_final: 0.7499 (tt) REVERT: A 707 TRP cc_start: 0.8618 (t-100) cc_final: 0.8336 (t-100) REVERT: A 766 GLN cc_start: 0.7797 (mm-40) cc_final: 0.7506 (mm-40) REVERT: B 803 TYR cc_start: 0.8771 (m-80) cc_final: 0.7752 (m-80) REVERT: B 807 ARG cc_start: 0.8023 (mtp-110) cc_final: 0.7775 (ttp80) REVERT: B 859 ILE cc_start: 0.8386 (mm) cc_final: 0.8018 (mm) REVERT: B 896 CYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7519 (m) outliers start: 6 outliers final: 4 residues processed: 60 average time/residue: 0.1889 time to fit residues: 14.0686 Evaluate side-chains 60 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 938 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.148910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.101073 restraints weight = 5363.691| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.52 r_work: 0.3259 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4092 Z= 0.316 Angle : 0.635 9.248 5569 Z= 0.326 Chirality : 0.047 0.221 628 Planarity : 0.005 0.048 724 Dihedral : 7.044 59.519 720 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer: Outliers : 1.18 % Allowed : 19.29 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.38), residues: 492 helix: -0.67 (0.83), residues: 38 sheet: -2.00 (0.40), residues: 144 loop : -2.20 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 699 HIS 0.005 0.001 HIS A 567 PHE 0.017 0.002 PHE A 681 TYR 0.010 0.001 TYR B 920 ARG 0.008 0.001 ARG B 807 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2316.06 seconds wall clock time: 41 minutes 40.78 seconds (2500.78 seconds total)