Starting phenix.real_space_refine on Thu Jul 18 22:22:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr7_32717/07_2024/7wr7_32717.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr7_32717/07_2024/7wr7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr7_32717/07_2024/7wr7_32717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr7_32717/07_2024/7wr7_32717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr7_32717/07_2024/7wr7_32717.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wr7_32717/07_2024/7wr7_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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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: 1.55 Conformation dependent library (CDL) restraints added in 683.7 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: 0.96 Time building geometry restraints manager: 1.71 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: 98.83 - 105.86: 108 105.86 - 112.89: 2193 112.89 - 119.92: 1303 119.92 - 126.94: 1897 126.94 - 133.97: 68 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 2.520 nonbonded pdb=" NH2 ARG B 908 " pdb=" O GLN B 978 " model vdw 2.350 2.520 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 2.520 nonbonded pdb=" O CYS B 826 " pdb=" NH1 ARG B 830 " model vdw 2.367 2.520 ... (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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.920 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.880 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 0.427 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: 0.2226 time to fit residues: 31.4297 Evaluate side-chains 77 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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: 3.9990 chunk 37 optimal weight: 0.3980 chunk 20 optimal weight: 0.0170 chunk 12 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 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 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 GLN ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 GLN B 938 ASN B 943 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4092 Z= 0.191 Angle : 0.559 9.260 5569 Z= 0.280 Chirality : 0.046 0.246 628 Planarity : 0.004 0.040 724 Dihedral : 7.710 56.448 728 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 3.29 % Allowed : 13.65 % Favored : 83.06 % 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: -3.79 (0.33), residues: 492 helix: -1.96 (0.68), residues: 38 sheet: -1.98 (0.41), residues: 107 loop : -2.98 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1013 HIS 0.004 0.001 HIS B 844 PHE 0.012 0.001 PHE A 693 TYR 0.008 0.001 TYR B 920 ARG 0.005 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 87 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 679 ARG cc_start: 0.8407 (ptp-170) cc_final: 0.8206 (mtm110) REVERT: A 766 GLN cc_start: 0.8001 (mm110) cc_final: 0.7770 (mm-40) REVERT: B 803 TYR cc_start: 0.7995 (m-80) cc_final: 0.7666 (m-80) REVERT: B 859 ILE cc_start: 0.8236 (mm) cc_final: 0.7890 (mm) REVERT: B 954 MET cc_start: 0.7441 (mtt) cc_final: 0.7168 (mtm) REVERT: B 959 TYR cc_start: 0.8019 (m-80) cc_final: 0.7576 (m-10) outliers start: 14 outliers final: 6 residues processed: 84 average time/residue: 0.2090 time to fit residues: 20.9368 Evaluate side-chains 74 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 HIS B 938 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4092 Z= 0.271 Angle : 0.585 9.279 5569 Z= 0.293 Chirality : 0.046 0.236 628 Planarity : 0.004 0.053 724 Dihedral : 7.354 57.566 723 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 3.76 % Allowed : 12.94 % 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: -3.63 (0.34), residues: 492 helix: -1.31 (0.77), residues: 38 sheet: -2.25 (0.37), residues: 132 loop : -2.77 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1013 HIS 0.010 0.001 HIS A 665 PHE 0.008 0.001 PHE A 537 TYR 0.008 0.001 TYR B 920 ARG 0.004 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 88 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 717 GLN cc_start: 0.8894 (pp30) cc_final: 0.8620 (pp30) REVERT: B 803 TYR cc_start: 0.8116 (m-80) cc_final: 0.7729 (m-80) REVERT: B 859 ILE cc_start: 0.8275 (mm) cc_final: 0.7913 (mm) outliers start: 16 outliers final: 11 residues processed: 83 average time/residue: 0.1981 time to fit residues: 19.7894 Evaluate side-chains 76 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 GLN Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 660 ASN 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 951 THR 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 23 optimal weight: 8.9990 chunk 4 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 44 optimal weight: 0.0370 chunk 47 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 39 optimal weight: 0.0970 chunk 26 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4092 Z= 0.156 Angle : 0.549 9.393 5569 Z= 0.277 Chirality : 0.045 0.236 628 Planarity : 0.004 0.044 724 Dihedral : 7.089 58.407 722 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 1.65 % Allowed : 16.71 % 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: -3.20 (0.35), residues: 492 helix: -0.96 (0.82), residues: 38 sheet: -1.58 (0.41), residues: 123 loop : -2.66 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 707 HIS 0.003 0.000 HIS A 567 PHE 0.010 0.001 PHE A 542 TYR 0.008 0.001 TYR B 920 ARG 0.006 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 70 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 ARG cc_start: 0.8454 (ptp-170) cc_final: 0.7817 (mtm110) REVERT: A 717 GLN cc_start: 0.8898 (pp30) cc_final: 0.8582 (pp30) REVERT: B 803 TYR cc_start: 0.8065 (m-80) cc_final: 0.7579 (m-80) REVERT: B 859 ILE cc_start: 0.8178 (mm) cc_final: 0.7837 (mm) outliers start: 7 outliers final: 7 residues processed: 69 average time/residue: 0.1898 time to fit residues: 16.1097 Evaluate side-chains 68 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 660 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.0010 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 ASN B 978 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4092 Z= 0.305 Angle : 0.596 9.232 5569 Z= 0.303 Chirality : 0.046 0.229 628 Planarity : 0.004 0.057 724 Dihedral : 7.251 58.408 722 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 3.06 % Allowed : 15.76 % Favored : 81.18 % 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: -3.27 (0.35), residues: 492 helix: -0.81 (0.83), residues: 38 sheet: -1.85 (0.39), residues: 132 loop : -2.64 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 798 HIS 0.005 0.001 HIS A 567 PHE 0.011 0.001 PHE A 542 TYR 0.008 0.001 TYR B1004 ARG 0.005 0.001 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 79 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 ARG cc_start: 0.8425 (ptp-170) cc_final: 0.7717 (mtm110) REVERT: A 717 GLN cc_start: 0.8920 (pp30) cc_final: 0.8593 (pp30) REVERT: B 803 TYR cc_start: 0.8209 (m-80) cc_final: 0.7627 (m-80) REVERT: B 859 ILE cc_start: 0.8266 (mm) cc_final: 0.7907 (mm) outliers start: 13 outliers final: 9 residues processed: 76 average time/residue: 0.1933 time to fit residues: 17.7709 Evaluate side-chains 71 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 0.0370 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN A 686 ASN ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 ASN B 978 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4092 Z= 0.212 Angle : 0.568 9.306 5569 Z= 0.287 Chirality : 0.045 0.231 628 Planarity : 0.004 0.047 724 Dihedral : 7.201 59.842 722 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 3.29 % Allowed : 16.24 % Favored : 80.47 % 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 (0.35), residues: 492 helix: -0.88 (0.82), residues: 38 sheet: -1.54 (0.41), residues: 119 loop : -2.62 (0.33), residues: 335 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 0.009 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 80 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7630 (tm-30) REVERT: A 717 GLN cc_start: 0.8935 (pp30) cc_final: 0.8589 (pp30) REVERT: B 803 TYR cc_start: 0.8182 (m-80) cc_final: 0.7573 (m-80) REVERT: B 859 ILE cc_start: 0.8198 (mm) cc_final: 0.7824 (mm) outliers start: 14 outliers final: 12 residues processed: 77 average time/residue: 0.1930 time to fit residues: 18.0116 Evaluate side-chains 74 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 660 ASN Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 772 CYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4092 Z= 0.327 Angle : 0.610 9.232 5569 Z= 0.312 Chirality : 0.047 0.227 628 Planarity : 0.005 0.063 724 Dihedral : 7.308 59.165 722 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.40 % Favored : 87.60 % Rotamer: Outliers : 2.82 % Allowed : 17.18 % 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: -3.29 (0.36), residues: 492 helix: -0.99 (0.81), residues: 38 sheet: -1.88 (0.40), residues: 132 loop : -2.61 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 707 HIS 0.005 0.001 HIS A 567 PHE 0.020 0.002 PHE A 681 TYR 0.009 0.001 TYR B 920 ARG 0.004 0.000 ARG A 692 *********************** 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 71 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 ARG cc_start: 0.8349 (ptp-170) cc_final: 0.7712 (mtm110) REVERT: B 803 TYR cc_start: 0.8242 (m-80) cc_final: 0.7598 (m-80) REVERT: B 859 ILE cc_start: 0.8303 (mm) cc_final: 0.7931 (mm) outliers start: 12 outliers final: 9 residues processed: 68 average time/residue: 0.1527 time to fit residues: 12.6951 Evaluate side-chains 69 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 678 VAL Chi-restraints excluded: chain A residue 772 CYS 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 23 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 26 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 943 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4092 Z= 0.220 Angle : 0.587 9.298 5569 Z= 0.299 Chirality : 0.046 0.228 628 Planarity : 0.004 0.048 724 Dihedral : 7.119 56.474 722 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 3.06 % Allowed : 17.41 % 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: -3.15 (0.36), residues: 492 helix: -1.25 (0.74), residues: 38 sheet: -1.51 (0.42), residues: 119 loop : -2.59 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 915 HIS 0.003 0.001 HIS A 567 PHE 0.029 0.002 PHE A 681 TYR 0.009 0.001 TYR B 920 ARG 0.012 0.001 ARG A 692 *********************** 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 73 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7987 (tm-30) REVERT: A 717 GLN cc_start: 0.8968 (pp30) cc_final: 0.8646 (pp30) REVERT: B 803 TYR cc_start: 0.8200 (m-80) cc_final: 0.7588 (m-80) REVERT: B 859 ILE cc_start: 0.8170 (mm) cc_final: 0.7776 (mm) outliers start: 13 outliers final: 10 residues processed: 71 average time/residue: 0.1839 time to fit residues: 16.0441 Evaluate side-chains 68 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 660 ASN Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 772 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4092 Z= 0.275 Angle : 0.604 9.251 5569 Z= 0.307 Chirality : 0.046 0.226 628 Planarity : 0.005 0.067 724 Dihedral : 7.181 58.236 722 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 3.29 % Allowed : 17.41 % Favored : 79.29 % 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: -3.14 (0.36), residues: 492 helix: -1.08 (0.80), residues: 38 sheet: -1.54 (0.42), residues: 119 loop : -2.58 (0.34), residues: 335 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 0.010 0.001 PHE A 542 TYR 0.009 0.001 TYR B 920 ARG 0.002 0.000 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 74 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 766 GLN cc_start: 0.7342 (mm-40) cc_final: 0.7133 (mm-40) REVERT: B 803 TYR cc_start: 0.8229 (m-80) cc_final: 0.7582 (m-80) REVERT: B 859 ILE cc_start: 0.8230 (mm) cc_final: 0.7841 (mm) outliers start: 14 outliers final: 11 residues processed: 70 average time/residue: 0.1873 time to fit residues: 16.0918 Evaluate side-chains 71 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 678 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 772 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4092 Z= 0.262 Angle : 0.610 9.258 5569 Z= 0.311 Chirality : 0.046 0.225 628 Planarity : 0.005 0.048 724 Dihedral : 7.159 59.476 722 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.80 % Favored : 87.20 % Rotamer: Outliers : 2.82 % Allowed : 18.12 % 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: -3.10 (0.36), residues: 492 helix: -1.00 (0.82), residues: 38 sheet: -1.55 (0.42), residues: 119 loop : -2.55 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 699 HIS 0.003 0.001 HIS A 567 PHE 0.010 0.001 PHE A 537 TYR 0.009 0.001 TYR B 920 ARG 0.004 0.001 ARG A 692 ********************** 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 69 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: B 803 TYR cc_start: 0.8302 (m-80) cc_final: 0.7596 (m-80) REVERT: B 859 ILE cc_start: 0.8221 (mm) cc_final: 0.7833 (mm) REVERT: B 896 CYS cc_start: 0.6397 (OUTLIER) cc_final: 0.6052 (m) outliers start: 12 outliers final: 8 residues processed: 68 average time/residue: 0.1895 time to fit residues: 15.9125 Evaluate side-chains 66 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 635 TYR Chi-restraints excluded: chain A residue 660 ASN Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 772 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.0570 chunk 34 optimal weight: 0.0070 chunk 2 optimal weight: 0.0870 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 overall best weight: 0.2494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 713 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 = 0.4044 r_free = 0.4044 target = 0.150486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.102209 restraints weight = 5349.718| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.57 r_work: 0.3297 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 4092 Z= 0.303 Angle : 1.285 59.194 5569 Z= 0.743 Chirality : 0.048 0.308 628 Planarity : 0.005 0.076 724 Dihedral : 7.152 59.529 722 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.80 % Favored : 87.20 % Rotamer: Outliers : 2.35 % Allowed : 18.35 % Favored : 79.29 % Cbeta Deviations : 0.22 % 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: -3.09 (0.36), residues: 492 helix: -1.00 (0.81), residues: 38 sheet: -1.55 (0.42), residues: 119 loop : -2.54 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 699 HIS 0.004 0.001 HIS A 567 PHE 0.009 0.001 PHE A 537 TYR 0.008 0.001 TYR B 920 ARG 0.002 0.000 ARG A 694 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1353.17 seconds wall clock time: 25 minutes 16.35 seconds (1516.35 seconds total)