Starting phenix.real_space_refine on Wed Jun 4 20:55:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wr7_32717/06_2025/7wr7_32717.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wr7_32717/06_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_32717/06_2025/7wr7_32717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wr7_32717/06_2025/7wr7_32717.map" model { file = "/net/cci-nas-00/data/ceres_data/7wr7_32717/06_2025/7wr7_32717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wr7_32717/06_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-5710/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: 3.18, per 1000 atoms: 0.80 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: 0.99 Conformation dependent library (CDL) restraints added in 384.4 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: 0.35 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: 0.88 Time building geometry restraints manager: 1.16 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: 0.010 Normalize map: mean=0, sd=1: 1.350 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.520 Find NCS groups from input model: 0.050 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.130 ------------------------------------------------------------------------------- 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 0.145 4110 Z= 0.304 Angle : 0.610 7.023 5612 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 9) link_NAG-ASN : angle 1.09755 ( 27) hydrogen bonds : bond 0.24605 ( 77) hydrogen bonds : angle 10.72767 ( 198) SS BOND : bond 0.00114 ( 8) SS BOND : angle 0.47116 ( 16) covalent geometry : bond 0.00369 ( 4092) covalent geometry : angle 0.60678 ( 5569) Misc. bond : bond 0.14536 ( 1) *********************** 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 : 0.401 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: 0.2208 time to fit residues: 31.1572 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 : 0.443 ------------------------------------------------------------------------------- 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: 4.9990 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 = 0.168899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.119393 restraints weight = 5064.345| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.35 r_work: 0.3607 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 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 4110 Z= 0.163 Angle : 0.621 9.545 5612 Z= 0.311 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 0.005 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 9) link_NAG-ASN : angle 1.30226 ( 27) hydrogen bonds : bond 0.04046 ( 77) hydrogen bonds : angle 6.71753 ( 198) SS BOND : bond 0.00445 ( 8) SS BOND : angle 1.05062 ( 16) covalent geometry : bond 0.00378 ( 4092) covalent geometry : angle 0.61378 ( 5569) Misc. bond : bond 0.00030 ( 1) *********************** 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 : 0.471 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: 0.8005 (t-100) REVERT: B 803 TYR cc_start: 0.8465 (m-80) cc_final: 0.7883 (m-80) REVERT: B 859 ILE cc_start: 0.8325 (mm) cc_final: 0.7943 (mm) REVERT: B 954 MET cc_start: 0.7451 (mtt) cc_final: 0.7213 (mtm) REVERT: B 1017 PHE cc_start: 0.7540 (m-10) cc_final: 0.7271 (m-10) outliers start: 13 outliers final: 6 residues processed: 80 average time/residue: 0.3455 time to fit residues: 32.8016 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 : 1.216 ------------------------------------------------------------------------------- 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: 6.9990 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4329 r_free = 0.4329 target = 0.177807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.128454 restraints weight = 5206.247| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 3.65 r_work: 0.3585 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4110 Z= 0.136 Angle : 0.586 9.399 5612 Z= 0.292 Chirality : 0.046 0.243 628 Planarity : 0.004 0.054 724 Dihedral : 6.968 55.901 721 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 2.59 % Allowed : 14.12 % 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: -3.52 (0.34), residues: 492 helix: -1.40 (0.75), residues: 38 sheet: -1.83 (0.39), residues: 117 loop : -2.84 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1013 HIS 0.003 0.001 HIS A 567 PHE 0.008 0.001 PHE A 627 TYR 0.007 0.001 TYR B 920 ARG 0.003 0.001 ARG A 692 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 9) link_NAG-ASN : angle 1.12590 ( 27) hydrogen bonds : bond 0.03324 ( 77) hydrogen bonds : angle 6.11072 ( 198) SS BOND : bond 0.00309 ( 8) SS BOND : angle 0.77466 ( 16) covalent geometry : bond 0.00318 ( 4092) covalent geometry : angle 0.58141 ( 5569) Misc. bond : bond 0.00029 ( 1) *********************** 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 79 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 540 THR cc_start: 0.8061 (OUTLIER) cc_final: 0.7835 (p) REVERT: A 679 ARG cc_start: 0.8723 (ptp-170) cc_final: 0.8226 (mtm110) REVERT: A 717 GLN cc_start: 0.8831 (pp30) cc_final: 0.8608 (pp30) REVERT: A 766 GLN cc_start: 0.7302 (mm-40) cc_final: 0.6992 (mm-40) REVERT: B 803 TYR cc_start: 0.8463 (m-80) cc_final: 0.7764 (m-80) REVERT: B 859 ILE cc_start: 0.8334 (mm) cc_final: 0.7977 (mm) outliers start: 11 outliers final: 8 residues processed: 77 average time/residue: 0.1665 time to fit residues: 16.0103 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 : 0.430 ------------------------------------------------------------------------------- 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 911 SER 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: 1.9990 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- 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 B 978 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.154962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.109409 restraints weight = 5420.674| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.33 r_work: 0.3449 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 4110 Z= 0.297 Angle : 0.693 9.171 5612 Z= 0.354 Chirality : 0.049 0.228 628 Planarity : 0.005 0.047 724 Dihedral : 7.371 57.448 721 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.40 % Favored : 87.60 % Rotamer: Outliers : 3.06 % Allowed : 15.29 % Favored : 81.65 % 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: -3.60 (0.35), residues: 492 helix: -1.13 (0.79), residues: 38 sheet: -2.25 (0.39), residues: 128 loop : -2.76 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 798 HIS 0.007 0.002 HIS A 567 PHE 0.013 0.002 PHE A 537 TYR 0.010 0.002 TYR B1004 ARG 0.005 0.001 ARG B 807 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 9) link_NAG-ASN : angle 1.36441 ( 27) hydrogen bonds : bond 0.03741 ( 77) hydrogen bonds : angle 6.50990 ( 198) SS BOND : bond 0.00581 ( 8) SS BOND : angle 1.10275 ( 16) covalent geometry : bond 0.00710 ( 4092) covalent geometry : angle 0.68694 ( 5569) Misc. bond : bond 0.00056 ( 1) *********************** 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 67 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7799 (tp) cc_final: 0.7479 (tt) REVERT: A 766 GLN cc_start: 0.7461 (mm-40) cc_final: 0.7161 (mm-40) REVERT: B 803 TYR cc_start: 0.8675 (m-80) cc_final: 0.7743 (m-80) REVERT: B 807 ARG cc_start: 0.8001 (mtp-110) cc_final: 0.7789 (mtp85) REVERT: B 859 ILE cc_start: 0.8452 (mm) cc_final: 0.8080 (mm) outliers start: 13 outliers final: 8 residues processed: 65 average time/residue: 0.2258 time to fit residues: 18.3825 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 : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.1980 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 27 optimal weight: 0.0170 chunk 42 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.157387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.108665 restraints weight = 5388.746| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.45 r_work: 0.3495 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4110 Z= 0.131 Angle : 0.592 9.413 5612 Z= 0.299 Chirality : 0.046 0.233 628 Planarity : 0.005 0.062 724 Dihedral : 6.962 57.901 720 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 2.12 % Allowed : 17.65 % 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: -3.26 (0.36), residues: 492 helix: -0.98 (0.82), residues: 38 sheet: -2.00 (0.40), residues: 134 loop : -2.52 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 915 HIS 0.003 0.001 HIS A 567 PHE 0.007 0.001 PHE A 627 TYR 0.020 0.001 TYR B 993 ARG 0.006 0.001 ARG B 940 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 9) link_NAG-ASN : angle 1.13098 ( 27) hydrogen bonds : bond 0.02869 ( 77) hydrogen bonds : angle 5.78215 ( 198) SS BOND : bond 0.00286 ( 8) SS BOND : angle 0.65206 ( 16) covalent geometry : bond 0.00303 ( 4092) covalent geometry : angle 0.58842 ( 5569) Misc. bond : bond 0.00014 ( 1) *********************** 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 70 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7644 (tp) cc_final: 0.7203 (tt) REVERT: A 679 ARG cc_start: 0.8741 (ptp-170) cc_final: 0.8465 (ptp-170) REVERT: A 766 GLN cc_start: 0.7582 (mm-40) cc_final: 0.7213 (mm-40) REVERT: B 803 TYR cc_start: 0.8610 (m-80) cc_final: 0.7640 (m-80) REVERT: B 859 ILE cc_start: 0.8330 (mm) cc_final: 0.7964 (mm) outliers start: 9 outliers final: 7 residues processed: 68 average time/residue: 0.1700 time to fit residues: 14.4565 Evaluate side-chains 65 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 809 LEU Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 896 CYS 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: 0.9980 chunk 21 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.145411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.101424 restraints weight = 5320.841| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.27 r_work: 0.3286 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 4110 Z= 0.238 Angle : 0.645 9.254 5612 Z= 0.327 Chirality : 0.047 0.226 628 Planarity : 0.004 0.045 724 Dihedral : 7.205 59.137 720 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.01 % Favored : 86.99 % 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: -3.40 (0.37), residues: 492 helix: -0.93 (0.82), residues: 38 sheet: -2.26 (0.39), residues: 144 loop : -2.53 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 798 HIS 0.005 0.001 HIS A 567 PHE 0.013 0.002 PHE A 537 TYR 0.012 0.002 TYR B 993 ARG 0.005 0.001 ARG A 692 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 9) link_NAG-ASN : angle 1.32549 ( 27) hydrogen bonds : bond 0.03239 ( 77) hydrogen bonds : angle 6.13999 ( 198) SS BOND : bond 0.00469 ( 8) SS BOND : angle 0.94635 ( 16) covalent geometry : bond 0.00569 ( 4092) covalent geometry : angle 0.63862 ( 5569) Misc. bond : bond 0.00103 ( 1) *********************** 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 72 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7763 (tp) cc_final: 0.7473 (tt) REVERT: A 766 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7432 (mm-40) REVERT: B 803 TYR cc_start: 0.8760 (m-80) cc_final: 0.7749 (m-80) REVERT: B 859 ILE cc_start: 0.8456 (mm) cc_final: 0.8059 (mm) outliers start: 12 outliers final: 7 residues processed: 68 average time/residue: 0.1748 time to fit residues: 14.8421 Evaluate side-chains 62 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 20 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.149904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.101515 restraints weight = 5391.265| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.59 r_work: 0.3303 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4110 Z= 0.153 Angle : 0.603 9.332 5612 Z= 0.305 Chirality : 0.046 0.229 628 Planarity : 0.005 0.068 724 Dihedral : 7.067 59.526 720 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 2.35 % Allowed : 18.12 % 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: -3.18 (0.37), residues: 492 helix: -0.91 (0.82), residues: 38 sheet: -1.99 (0.40), residues: 144 loop : -2.43 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 915 HIS 0.003 0.001 HIS A 567 PHE 0.023 0.002 PHE A 681 TYR 0.010 0.001 TYR B 920 ARG 0.008 0.001 ARG B 807 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 9) link_NAG-ASN : angle 1.18080 ( 27) hydrogen bonds : bond 0.02836 ( 77) hydrogen bonds : angle 5.82083 ( 198) SS BOND : bond 0.00307 ( 8) SS BOND : angle 0.66292 ( 16) covalent geometry : bond 0.00361 ( 4092) covalent geometry : angle 0.59841 ( 5569) Misc. bond : bond 0.00061 ( 1) *********************** 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 69 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7787 (tp) cc_final: 0.7421 (tt) REVERT: A 679 ARG cc_start: 0.8704 (ptp-170) cc_final: 0.7808 (mtm110) REVERT: A 766 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7480 (mm-40) REVERT: B 803 TYR cc_start: 0.8746 (m-80) cc_final: 0.7681 (m-80) REVERT: B 859 ILE cc_start: 0.8374 (mm) cc_final: 0.7987 (mm) REVERT: B 896 CYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7386 (m) outliers start: 10 outliers final: 6 residues processed: 65 average time/residue: 0.2511 time to fit residues: 20.0867 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 : 1.037 ------------------------------------------------------------------------------- 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 809 LEU 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: 0.0670 chunk 23 optimal weight: 0.0060 chunk 43 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.0170 chunk 9 optimal weight: 0.5980 overall best weight: 0.3172 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.158778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.111284 restraints weight = 5194.427| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.38 r_work: 0.3521 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4110 Z= 0.113 Angle : 0.587 9.402 5612 Z= 0.297 Chirality : 0.045 0.228 628 Planarity : 0.004 0.048 724 Dihedral : 6.848 58.999 720 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 2.12 % Allowed : 18.35 % 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: -2.85 (0.37), residues: 492 helix: -0.81 (0.82), residues: 38 sheet: -1.47 (0.43), residues: 130 loop : -2.33 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 915 HIS 0.002 0.000 HIS A 567 PHE 0.026 0.001 PHE A 681 TYR 0.008 0.001 TYR B 920 ARG 0.010 0.001 ARG A 692 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 9) link_NAG-ASN : angle 1.13541 ( 27) hydrogen bonds : bond 0.02569 ( 77) hydrogen bonds : angle 5.40505 ( 198) SS BOND : bond 0.00207 ( 8) SS BOND : angle 0.54417 ( 16) covalent geometry : bond 0.00256 ( 4092) covalent geometry : angle 0.58348 ( 5569) Misc. bond : bond 0.00029 ( 1) *********************** 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 70 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7769 (tp) cc_final: 0.7336 (tt) REVERT: A 693 PHE cc_start: 0.8670 (m-80) cc_final: 0.8411 (m-80) REVERT: A 717 GLN cc_start: 0.8985 (pp30) cc_final: 0.8644 (pp30) REVERT: A 718 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8127 (mp) REVERT: A 766 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7531 (mm-40) REVERT: B 803 TYR cc_start: 0.8583 (m-80) cc_final: 0.7576 (m-80) REVERT: B 859 ILE cc_start: 0.8299 (mm) cc_final: 0.7946 (mm) REVERT: B 959 TYR cc_start: 0.8194 (m-80) cc_final: 0.7500 (m-10) outliers start: 9 outliers final: 6 residues processed: 67 average time/residue: 0.2098 time to fit residues: 18.1464 Evaluate side-chains 65 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 718 LEU Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 896 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 0.0010 chunk 13 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.148652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.100197 restraints weight = 5405.541| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.57 r_work: 0.3283 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4110 Z= 0.215 Angle : 0.649 9.265 5612 Z= 0.334 Chirality : 0.048 0.224 628 Planarity : 0.004 0.047 724 Dihedral : 7.032 59.632 720 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.40 % Favored : 87.60 % Rotamer: Outliers : 3.06 % Allowed : 18.12 % 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 (0.38), residues: 492 helix: -0.75 (0.83), residues: 38 sheet: -1.96 (0.40), residues: 145 loop : -2.21 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 798 HIS 0.005 0.001 HIS A 567 PHE 0.030 0.002 PHE A 681 TYR 0.010 0.001 TYR B 920 ARG 0.016 0.001 ARG A 692 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 9) link_NAG-ASN : angle 1.35740 ( 27) hydrogen bonds : bond 0.03050 ( 77) hydrogen bonds : angle 5.80529 ( 198) SS BOND : bond 0.00404 ( 8) SS BOND : angle 0.86920 ( 16) covalent geometry : bond 0.00511 ( 4092) covalent geometry : angle 0.64327 ( 5569) Misc. bond : bond 0.00097 ( 1) *********************** 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 69 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7933 (tp) cc_final: 0.7565 (tt) REVERT: A 766 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7551 (mm-40) REVERT: B 803 TYR cc_start: 0.8799 (m-80) cc_final: 0.7750 (m-80) REVERT: B 859 ILE cc_start: 0.8445 (mm) cc_final: 0.8034 (mm) REVERT: B 896 CYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7516 (m) outliers start: 13 outliers final: 7 residues processed: 64 average time/residue: 0.1667 time to fit residues: 13.3829 Evaluate side-chains 64 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 889 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 955 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 0.1980 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 17 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.149937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.102280 restraints weight = 5369.299| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.58 r_work: 0.3315 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4110 Z= 0.149 Angle : 0.637 9.315 5612 Z= 0.321 Chirality : 0.047 0.223 628 Planarity : 0.004 0.049 724 Dihedral : 6.935 58.483 720 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 1.65 % Allowed : 18.59 % 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: -2.87 (0.38), residues: 492 helix: -0.71 (0.83), residues: 38 sheet: -1.90 (0.40), residues: 145 loop : -2.13 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 798 HIS 0.003 0.001 HIS A 567 PHE 0.034 0.002 PHE A 681 TYR 0.009 0.001 TYR B 920 ARG 0.005 0.000 ARG A 692 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 9) link_NAG-ASN : angle 1.24065 ( 27) hydrogen bonds : bond 0.02748 ( 77) hydrogen bonds : angle 5.60917 ( 198) SS BOND : bond 0.00305 ( 8) SS BOND : angle 0.58852 ( 16) covalent geometry : bond 0.00348 ( 4092) covalent geometry : angle 0.63331 ( 5569) Misc. bond : bond 0.00055 ( 1) ********************** 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 64 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7917 (tp) cc_final: 0.7530 (tt) REVERT: A 766 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7541 (mm-40) REVERT: B 803 TYR cc_start: 0.8753 (m-80) cc_final: 0.7719 (m-80) REVERT: B 859 ILE cc_start: 0.8384 (mm) cc_final: 0.8008 (mm) REVERT: B 896 CYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7557 (m) REVERT: B 959 TYR cc_start: 0.8180 (m-10) cc_final: 0.7642 (m-10) outliers start: 7 outliers final: 5 residues processed: 61 average time/residue: 0.1870 time to fit residues: 14.2195 Evaluate side-chains 60 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 739 VAL Chi-restraints excluded: chain A residue 781 ILE 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 23 optimal weight: 9.9990 chunk 39 optimal weight: 0.3980 chunk 19 optimal weight: 0.4980 chunk 22 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4006 r_free = 0.4006 target = 0.146687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.102994 restraints weight = 5234.369| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.32 r_work: 0.3310 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4110 Z= 0.188 Angle : 0.671 9.265 5612 Z= 0.339 Chirality : 0.047 0.222 628 Planarity : 0.004 0.047 724 Dihedral : 7.061 59.118 720 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 1.88 % Allowed : 18.35 % 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: -2.87 (0.38), residues: 492 helix: -0.69 (0.82), residues: 38 sheet: -1.82 (0.41), residues: 132 loop : -2.20 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 699 HIS 0.004 0.001 HIS A 567 PHE 0.042 0.002 PHE A 681 TYR 0.010 0.001 TYR B 920 ARG 0.008 0.000 ARG A 692 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 9) link_NAG-ASN : angle 1.38935 ( 27) hydrogen bonds : bond 0.02925 ( 77) hydrogen bonds : angle 5.70591 ( 198) SS BOND : bond 0.00373 ( 8) SS BOND : angle 0.74332 ( 16) covalent geometry : bond 0.00447 ( 4092) covalent geometry : angle 0.66580 ( 5569) Misc. bond : bond 0.00080 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2664.24 seconds wall clock time: 48 minutes 28.80 seconds (2908.80 seconds total)