Starting phenix.real_space_refine on Fri Aug 22 14:29:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wqx_32715/08_2025/7wqx_32715.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wqx_32715/08_2025/7wqx_32715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wqx_32715/08_2025/7wqx_32715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wqx_32715/08_2025/7wqx_32715.map" model { file = "/net/cci-nas-00/data/ceres_data/7wqx_32715/08_2025/7wqx_32715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wqx_32715/08_2025/7wqx_32715.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.011 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 2525 2.51 5 N 683 2.21 5 O 785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4022 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3896 Classifications: {'peptide': 501} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 470} Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 1.15, per 1000 atoms: 0.29 Number of scatterers: 4022 At special positions: 0 Unit cell: (63.806, 81.588, 103.554, 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 785 8.00 N 683 7.00 C 2525 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 643 " - pdb=" SG CYS A 655 " distance=2.03 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 A 896 " distance=2.03 Simple disulfide: pdb=" SG CYS A 810 " - pdb=" SG CYS A 826 " distance=2.03 Simple disulfide: pdb=" SG CYS A 910 " - pdb=" SG CYS A 977 " distance=2.03 Simple disulfide: pdb=" SG CYS A 941 " - pdb=" SG CYS A 956 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 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=0, symmetry=0 Links applied NAG-ASN " NAG A1101 " - " ASN A 909 " " NAG A1102 " - " ASN A 534 " " NAG A1103 " - " ASN A 630 " " NAG A1104 " - " ASN A 682 " " NAG A1105 " - " ASN A 706 " " NAG A1106 " - " ASN A 848 " " NAG A1107 " - " ASN A 887 " " NAG A1108 " - " ASN A 949 " " NAG A1109 " - " ASN A 725 " Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 150.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 914 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 9 sheets defined 7.4% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 659 through 661 No H-bonds generated for 'chain 'A' and resid 659 through 661' Processing helix chain 'A' and resid 711 through 719 Processing helix chain 'A' and resid 833 through 835 No H-bonds generated for 'chain 'A' and resid 833 through 835' Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 1007 through 1009 No H-bonds generated for 'chain 'A' and resid 1007 through 1009' Processing helix chain 'A' and resid 1010 through 1019 removed outlier: 3.798A pdb=" N PHE A1017 " --> pdb=" O TRP A1013 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS A1019 " --> pdb=" O GLN A1015 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 529 through 530 removed outlier: 3.677A pdb=" N CYS A 552 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 529 through 530 Processing sheet with id=AA3, first strand: chain 'A' and resid 536 through 538 removed outlier: 7.390A pdb=" N GLY A 626 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N PHE A 571 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LYS A 628 " --> pdb=" O GLN A 569 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS A 567 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY A 634 " --> pdb=" O ASN A 563 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 647 through 649 Processing sheet with id=AA5, first strand: chain 'A' and resid 688 through 689 removed outlier: 7.040A pdb=" N GLN A 766 " --> pdb=" O ASN A 725 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 693 through 695 Processing sheet with id=AA7, first strand: chain 'A' and resid 740 through 742 removed outlier: 3.610A pdb=" N LYS A 740 " --> pdb=" O THR A 752 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 750 " --> pdb=" O ASN A 742 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 799 through 804 removed outlier: 3.988A pdb=" N GLU A 861 " --> pdb=" O HIS A 881 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE A 859 " --> pdb=" O TRP A 837 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TRP A 837 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 909 through 914 removed outlier: 3.533A pdb=" N ALA A 931 " --> pdb=" O ILE A 912 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N CYS A 956 " --> pdb=" O LEU A 936 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL A1003 " --> pdb=" O SER A 990 " (cutoff:3.500A) 85 hydrogen bonds defined for protein. 216 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: 0.68 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1326 1.34 - 1.46: 844 1.46 - 1.58: 1915 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 4121 Sorted by residual: bond pdb=" C1 NAG A1103 " pdb=" O5 NAG A1103 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C1 NAG A1101 " pdb=" O5 NAG A1101 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C1 NAG A1105 " pdb=" O5 NAG A1105 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C1 NAG A1108 " pdb=" O5 NAG A1108 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C5 NAG A1103 " pdb=" O5 NAG A1103 " ideal model delta sigma weight residual 1.413 1.441 -0.028 2.00e-02 2.50e+03 1.93e+00 ... (remaining 4116 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 5382 1.17 - 2.35: 170 2.35 - 3.52: 55 3.52 - 4.70: 5 4.70 - 5.87: 1 Bond angle restraints: 5613 Sorted by residual: angle pdb=" N ILE A 785 " pdb=" CA ILE A 785 " pdb=" C ILE A 785 " ideal model delta sigma weight residual 111.67 109.37 2.30 9.50e-01 1.11e+00 5.87e+00 angle pdb=" N LYS A 784 " pdb=" CA LYS A 784 " pdb=" C LYS A 784 " ideal model delta sigma weight residual 107.23 110.82 -3.59 1.67e+00 3.59e-01 4.62e+00 angle pdb=" C1 NAG A1103 " pdb=" O5 NAG A1103 " pdb=" C5 NAG A1103 " ideal model delta sigma weight residual 113.21 119.08 -5.87 3.00e+00 1.11e-01 3.83e+00 angle pdb=" CA ASN A 848 " pdb=" C ASN A 848 " pdb=" O ASN A 848 " ideal model delta sigma weight residual 120.27 122.63 -2.36 1.24e+00 6.50e-01 3.61e+00 angle pdb=" N ILE A 895 " pdb=" CA ILE A 895 " pdb=" C ILE A 895 " ideal model delta sigma weight residual 110.05 108.20 1.85 1.09e+00 8.42e-01 2.88e+00 ... (remaining 5608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.92: 2486 22.92 - 45.84: 61 45.84 - 68.75: 22 68.75 - 91.67: 2 91.67 - 114.59: 3 Dihedral angle restraints: 2574 sinusoidal: 1146 harmonic: 1428 Sorted by residual: dihedral pdb=" C1 NAG A1103 " pdb=" C5 NAG A1103 " pdb=" O5 NAG A1103 " pdb=" C4 NAG A1103 " ideal model delta sinusoidal sigma weight residual -64.11 50.48 -114.59 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" C1 NAG A1103 " pdb=" C5 NAG A1103 " pdb=" O5 NAG A1103 " pdb=" C6 NAG A1103 " ideal model delta sinusoidal sigma weight residual 171.16 -74.39 -114.45 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" C2 NAG A1103 " pdb=" C1 NAG A1103 " pdb=" O5 NAG A1103 " pdb=" C5 NAG A1103 " ideal model delta sinusoidal sigma weight residual -62.96 42.61 -105.57 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 2571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 421 0.036 - 0.073: 138 0.073 - 0.109: 57 0.109 - 0.145: 16 0.145 - 0.182: 3 Chirality restraints: 635 Sorted by residual: chirality pdb=" C1 NAG A1103 " pdb=" ND2 ASN A 630 " pdb=" C2 NAG A1103 " pdb=" O5 NAG A1103 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" C2 NAG A1102 " pdb=" C1 NAG A1102 " pdb=" C3 NAG A1102 " pdb=" N2 NAG A1102 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" C1 NAG A1104 " pdb=" ND2 ASN A 682 " pdb=" C2 NAG A1104 " pdb=" O5 NAG A1104 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 632 not shown) Planarity restraints: 740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 855 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO A 856 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 856 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 856 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " 0.016 5.00e-02 4.00e+02 2.49e-02 9.90e-01 pdb=" N PRO A 527 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 997 " -0.015 5.00e-02 4.00e+02 2.26e-02 8.14e-01 pdb=" N PRO A 998 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 998 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 998 " -0.013 5.00e-02 4.00e+02 ... (remaining 737 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 230 2.72 - 3.27: 3941 3.27 - 3.81: 6361 3.81 - 4.36: 7670 4.36 - 4.90: 13046 Nonbonded interactions: 31248 Sorted by model distance: nonbonded pdb=" OD1 ASP A 584 " pdb=" OG1 THR A 609 " model vdw 2.181 3.040 nonbonded pdb=" OD2 ASP A 874 " pdb=" ND2 ASN A 875 " model vdw 2.315 3.120 nonbonded pdb=" OD2 ASP A 584 " pdb=" OG SER A 607 " model vdw 2.316 3.040 nonbonded pdb=" OD1 ASP A 670 " pdb=" OG SER A 672 " model vdw 2.322 3.040 nonbonded pdb=" NE2 GLN A 902 " pdb=" OE1 GLU A 979 " model vdw 2.341 3.120 ... (remaining 31243 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.760 Find NCS groups from input model: 0.020 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:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 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 : 0.003 0.081 4139 Z= 0.166 Angle : 0.531 5.875 5658 Z= 0.279 Chirality : 0.045 0.182 635 Planarity : 0.003 0.030 731 Dihedral : 11.771 114.590 1633 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.56 % Allowed : 7.21 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.61 (0.30), residues: 499 helix: -2.67 (0.54), residues: 35 sheet: -2.54 (0.36), residues: 133 loop : -2.41 (0.29), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 583 TYR 0.004 0.000 TYR A 546 PHE 0.005 0.001 PHE A 693 TRP 0.004 0.001 TRP A 699 HIS 0.001 0.000 HIS A 825 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4121) covalent geometry : angle 0.52609 ( 5613) SS BOND : bond 0.00101 ( 9) SS BOND : angle 0.50180 ( 18) hydrogen bonds : bond 0.17249 ( 81) hydrogen bonds : angle 6.96547 ( 216) link_NAG-ASN : bond 0.00235 ( 9) link_NAG-ASN : angle 1.13232 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7737 (mt) cc_final: 0.7481 (tm) REVERT: A 635 TYR cc_start: 0.7168 (m-80) cc_final: 0.6717 (m-80) REVERT: A 651 LYS cc_start: 0.8311 (mmmt) cc_final: 0.7958 (mppt) REVERT: A 750 ILE cc_start: 0.6160 (tp) cc_final: 0.5800 (mp) REVERT: A 927 ILE cc_start: 0.6968 (mt) cc_final: 0.6641 (mt) outliers start: 11 outliers final: 1 residues processed: 108 average time/residue: 0.4678 time to fit residues: 52.4278 Evaluate side-chains 76 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 993 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.0770 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.0070 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 HIS A 649 GLN A 665 HIS ** A 667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN ** A 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 HIS A 875 ASN ** A 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.162175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.147465 restraints weight = 7941.783| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 3.07 r_work: 0.4174 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4139 Z= 0.138 Angle : 0.688 11.869 5658 Z= 0.331 Chirality : 0.049 0.203 635 Planarity : 0.004 0.026 731 Dihedral : 11.174 87.987 725 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.26 % Allowed : 14.42 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.34), residues: 499 helix: -1.43 (0.74), residues: 35 sheet: -1.65 (0.43), residues: 115 loop : -1.80 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 872 TYR 0.010 0.001 TYR A 804 PHE 0.011 0.001 PHE A 537 TRP 0.011 0.001 TRP A 707 HIS 0.003 0.001 HIS A 844 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4121) covalent geometry : angle 0.66693 ( 5613) SS BOND : bond 0.00390 ( 9) SS BOND : angle 2.61927 ( 18) hydrogen bonds : bond 0.03902 ( 81) hydrogen bonds : angle 5.38858 ( 216) link_NAG-ASN : bond 0.00205 ( 9) link_NAG-ASN : angle 1.45077 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 ASP cc_start: 0.6999 (p0) cc_final: 0.6772 (p0) REVERT: A 635 TYR cc_start: 0.7611 (m-80) cc_final: 0.7281 (m-80) REVERT: A 651 LYS cc_start: 0.8390 (mmmt) cc_final: 0.8078 (mmtm) REVERT: A 750 ILE cc_start: 0.6024 (tp) cc_final: 0.5749 (mp) REVERT: A 804 TYR cc_start: 0.8061 (t80) cc_final: 0.7662 (t80) REVERT: A 845 MET cc_start: 0.6503 (mmm) cc_final: 0.6110 (mmt) REVERT: A 894 PRO cc_start: 0.8701 (Cg_endo) cc_final: 0.8497 (Cg_exo) REVERT: A 899 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6797 (pp20) REVERT: A 927 ILE cc_start: 0.7216 (mt) cc_final: 0.6883 (tt) outliers start: 14 outliers final: 6 residues processed: 86 average time/residue: 0.4929 time to fit residues: 43.9623 Evaluate side-chains 77 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 677 CYS Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 993 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 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 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS A 647 HIS ** A 667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN ** A 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.158475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.143789 restraints weight = 7848.517| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 3.07 r_work: 0.4127 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4139 Z= 0.182 Angle : 0.723 10.562 5658 Z= 0.344 Chirality : 0.049 0.198 635 Planarity : 0.004 0.028 731 Dihedral : 8.939 57.997 725 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.02 % Allowed : 16.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.34), residues: 499 helix: -1.45 (0.73), residues: 35 sheet: -1.66 (0.45), residues: 107 loop : -1.62 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 872 TYR 0.010 0.001 TYR A 546 PHE 0.008 0.001 PHE A 542 TRP 0.017 0.002 TRP A 707 HIS 0.009 0.002 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 4121) covalent geometry : angle 0.69555 ( 5613) SS BOND : bond 0.00326 ( 9) SS BOND : angle 2.00511 ( 18) hydrogen bonds : bond 0.03630 ( 81) hydrogen bonds : angle 5.52474 ( 216) link_NAG-ASN : bond 0.00395 ( 9) link_NAG-ASN : angle 2.48903 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8020 (m) REVERT: A 635 TYR cc_start: 0.7635 (m-80) cc_final: 0.7304 (m-80) REVERT: A 651 LYS cc_start: 0.8439 (mmmt) cc_final: 0.7977 (mttt) REVERT: A 679 ARG cc_start: 0.5970 (mtm110) cc_final: 0.5141 (mtm110) REVERT: A 692 ARG cc_start: 0.5476 (ptp-110) cc_final: 0.5255 (ptp-110) REVERT: A 750 ILE cc_start: 0.5877 (tp) cc_final: 0.5627 (mp) REVERT: A 793 GLU cc_start: 0.5780 (OUTLIER) cc_final: 0.5556 (pm20) REVERT: A 845 MET cc_start: 0.6627 (mmm) cc_final: 0.6297 (mmt) outliers start: 13 outliers final: 3 residues processed: 87 average time/residue: 0.4769 time to fit residues: 43.0919 Evaluate side-chains 76 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 993 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 0.0870 chunk 6 optimal weight: 0.8980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 HIS A 742 ASN ** A 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 929 GLN ** A 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.159275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.144654 restraints weight = 7744.364| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 3.03 r_work: 0.4141 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4139 Z= 0.141 Angle : 0.665 9.660 5658 Z= 0.321 Chirality : 0.049 0.199 635 Planarity : 0.004 0.035 731 Dihedral : 8.195 59.238 725 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.02 % Allowed : 18.37 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.22 (0.34), residues: 499 helix: -1.17 (0.77), residues: 35 sheet: -1.59 (0.43), residues: 115 loop : -1.52 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 872 TYR 0.011 0.001 TYR A 948 PHE 0.008 0.001 PHE A 542 TRP 0.024 0.002 TRP A 699 HIS 0.008 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4121) covalent geometry : angle 0.64150 ( 5613) SS BOND : bond 0.00339 ( 9) SS BOND : angle 1.49637 ( 18) hydrogen bonds : bond 0.03144 ( 81) hydrogen bonds : angle 5.38564 ( 216) link_NAG-ASN : bond 0.00203 ( 9) link_NAG-ASN : angle 2.35510 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 TYR cc_start: 0.7594 (m-80) cc_final: 0.7286 (m-80) REVERT: A 639 ILE cc_start: 0.7582 (tp) cc_final: 0.7240 (pp) REVERT: A 651 LYS cc_start: 0.8370 (mmmt) cc_final: 0.7946 (mttt) REVERT: A 750 ILE cc_start: 0.5905 (tp) cc_final: 0.5647 (mp) REVERT: A 793 GLU cc_start: 0.5830 (OUTLIER) cc_final: 0.5621 (pm20) REVERT: A 813 SER cc_start: 0.8638 (m) cc_final: 0.8125 (p) outliers start: 13 outliers final: 3 residues processed: 84 average time/residue: 0.4357 time to fit residues: 38.0903 Evaluate side-chains 76 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 993 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 0.0870 chunk 1 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 0.0570 chunk 45 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 38 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 HIS A 742 ASN ** A 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.159965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.145397 restraints weight = 7783.865| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 3.07 r_work: 0.4153 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4139 Z= 0.122 Angle : 0.655 9.650 5658 Z= 0.321 Chirality : 0.048 0.216 635 Planarity : 0.004 0.030 731 Dihedral : 8.047 59.669 725 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.56 % Allowed : 19.07 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.36), residues: 499 helix: -0.83 (0.83), residues: 35 sheet: -1.60 (0.41), residues: 134 loop : -1.30 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1000 TYR 0.011 0.001 TYR A 888 PHE 0.010 0.001 PHE A 680 TRP 0.027 0.002 TRP A 699 HIS 0.008 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4121) covalent geometry : angle 0.63325 ( 5613) SS BOND : bond 0.00248 ( 9) SS BOND : angle 1.68212 ( 18) hydrogen bonds : bond 0.02864 ( 81) hydrogen bonds : angle 5.25758 ( 216) link_NAG-ASN : bond 0.00245 ( 9) link_NAG-ASN : angle 2.15966 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 635 TYR cc_start: 0.7527 (m-80) cc_final: 0.7311 (m-80) REVERT: A 639 ILE cc_start: 0.7547 (tp) cc_final: 0.7232 (pp) REVERT: A 651 LYS cc_start: 0.8402 (mmmt) cc_final: 0.7942 (mttt) REVERT: A 750 ILE cc_start: 0.6020 (OUTLIER) cc_final: 0.5761 (mp) REVERT: A 813 SER cc_start: 0.8630 (m) cc_final: 0.8129 (p) REVERT: A 899 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6706 (pp20) REVERT: A 1015 GLN cc_start: 0.8340 (mm-40) cc_final: 0.8106 (mm-40) outliers start: 11 outliers final: 3 residues processed: 84 average time/residue: 0.4316 time to fit residues: 37.8578 Evaluate side-chains 76 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 993 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 ASN ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS A 742 ASN ** A 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.156674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.141944 restraints weight = 7854.907| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 3.08 r_work: 0.4101 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4139 Z= 0.204 Angle : 0.746 9.822 5658 Z= 0.363 Chirality : 0.051 0.207 635 Planarity : 0.004 0.034 731 Dihedral : 8.527 58.711 725 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.33 % Allowed : 20.47 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.35), residues: 499 helix: -1.18 (0.79), residues: 35 sheet: -1.58 (0.43), residues: 134 loop : -1.48 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 872 TYR 0.011 0.001 TYR A 546 PHE 0.019 0.002 PHE A 680 TRP 0.020 0.002 TRP A 707 HIS 0.008 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 4121) covalent geometry : angle 0.71716 ( 5613) SS BOND : bond 0.00474 ( 9) SS BOND : angle 2.04715 ( 18) hydrogen bonds : bond 0.03517 ( 81) hydrogen bonds : angle 5.66182 ( 216) link_NAG-ASN : bond 0.00457 ( 9) link_NAG-ASN : angle 2.65428 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 557 ASN cc_start: 0.7167 (m110) cc_final: 0.6836 (m110) REVERT: A 639 ILE cc_start: 0.7683 (tp) cc_final: 0.7338 (pp) REVERT: A 651 LYS cc_start: 0.8483 (mmmt) cc_final: 0.7949 (mppt) REVERT: A 750 ILE cc_start: 0.5844 (OUTLIER) cc_final: 0.5628 (mp) REVERT: A 776 LEU cc_start: 0.7989 (mt) cc_final: 0.7777 (mp) REVERT: A 793 GLU cc_start: 0.5830 (OUTLIER) cc_final: 0.5627 (pm20) REVERT: A 1015 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8133 (mm-40) outliers start: 10 outliers final: 6 residues processed: 81 average time/residue: 0.4312 time to fit residues: 36.5117 Evaluate side-chains 79 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 993 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 0.0980 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.0670 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS ** A 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 929 GLN A 980 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.158032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.143060 restraints weight = 7877.275| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 3.14 r_work: 0.4121 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4139 Z= 0.140 Angle : 0.680 9.660 5658 Z= 0.329 Chirality : 0.048 0.195 635 Planarity : 0.004 0.034 731 Dihedral : 8.270 59.915 725 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.26 % Allowed : 20.70 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.35), residues: 499 helix: -1.00 (0.82), residues: 35 sheet: -1.23 (0.47), residues: 115 loop : -1.47 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 872 TYR 0.012 0.001 TYR A 888 PHE 0.012 0.001 PHE A 680 TRP 0.014 0.002 TRP A 707 HIS 0.009 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4121) covalent geometry : angle 0.64783 ( 5613) SS BOND : bond 0.00357 ( 9) SS BOND : angle 2.51853 ( 18) hydrogen bonds : bond 0.02993 ( 81) hydrogen bonds : angle 5.48475 ( 216) link_NAG-ASN : bond 0.00201 ( 9) link_NAG-ASN : angle 2.30277 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7898 (mt) cc_final: 0.7472 (tm) REVERT: A 557 ASN cc_start: 0.7134 (m110) cc_final: 0.6798 (m110) REVERT: A 639 ILE cc_start: 0.7721 (tp) cc_final: 0.7435 (pp) REVERT: A 651 LYS cc_start: 0.8453 (mmmt) cc_final: 0.7923 (mppt) REVERT: A 750 ILE cc_start: 0.5816 (OUTLIER) cc_final: 0.5601 (mp) REVERT: A 776 LEU cc_start: 0.7916 (mt) cc_final: 0.7707 (mp) REVERT: A 899 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6495 (pp20) REVERT: A 1015 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8075 (mm-40) outliers start: 14 outliers final: 6 residues processed: 81 average time/residue: 0.3352 time to fit residues: 28.4592 Evaluate side-chains 74 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 993 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 37 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS ** A 769 HIS ** 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 = 0.4373 r_free = 0.4373 target = 0.157442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.142828 restraints weight = 7713.922| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 3.04 r_work: 0.4117 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4139 Z= 0.160 Angle : 0.703 9.704 5658 Z= 0.342 Chirality : 0.049 0.193 635 Planarity : 0.004 0.039 731 Dihedral : 8.360 59.436 725 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.33 % Allowed : 22.09 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.36), residues: 499 helix: -1.06 (0.81), residues: 35 sheet: -1.51 (0.44), residues: 131 loop : -1.47 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 872 TYR 0.009 0.001 TYR A 546 PHE 0.012 0.001 PHE A 542 TRP 0.017 0.002 TRP A 707 HIS 0.008 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 4121) covalent geometry : angle 0.67595 ( 5613) SS BOND : bond 0.00415 ( 9) SS BOND : angle 2.02262 ( 18) hydrogen bonds : bond 0.03072 ( 81) hydrogen bonds : angle 5.54771 ( 216) link_NAG-ASN : bond 0.00284 ( 9) link_NAG-ASN : angle 2.40705 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7984 (mt) cc_final: 0.7563 (tm) REVERT: A 557 ASN cc_start: 0.7084 (m110) cc_final: 0.6723 (m110) REVERT: A 639 ILE cc_start: 0.7750 (tp) cc_final: 0.7447 (pp) REVERT: A 651 LYS cc_start: 0.8466 (mmmt) cc_final: 0.7942 (mppt) REVERT: A 739 VAL cc_start: 0.6227 (p) cc_final: 0.4774 (t) REVERT: A 750 ILE cc_start: 0.5833 (OUTLIER) cc_final: 0.5612 (mp) REVERT: A 776 LEU cc_start: 0.7949 (mt) cc_final: 0.7738 (mp) REVERT: A 899 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6505 (pp20) REVERT: A 982 ARG cc_start: 0.6007 (OUTLIER) cc_final: 0.5773 (ttt180) REVERT: A 1000 ARG cc_start: 0.6351 (mpt180) cc_final: 0.5932 (tpp-160) REVERT: A 1015 GLN cc_start: 0.8293 (mm-40) cc_final: 0.8033 (mm-40) outliers start: 10 outliers final: 6 residues processed: 79 average time/residue: 0.4035 time to fit residues: 33.3451 Evaluate side-chains 78 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 982 ARG Chi-restraints excluded: chain A residue 993 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 0.0770 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.0770 chunk 8 optimal weight: 0.8980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 ASN A 636 HIS ** A 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.158236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.143992 restraints weight = 7846.335| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 2.97 r_work: 0.4129 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4139 Z= 0.138 Angle : 0.677 9.642 5658 Z= 0.333 Chirality : 0.048 0.200 635 Planarity : 0.005 0.066 731 Dihedral : 8.267 59.885 725 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.26 % Allowed : 22.09 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.36), residues: 499 helix: -1.03 (0.81), residues: 35 sheet: -1.47 (0.44), residues: 133 loop : -1.42 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 872 TYR 0.015 0.001 TYR A 888 PHE 0.013 0.001 PHE A 542 TRP 0.017 0.002 TRP A 707 HIS 0.008 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 4121) covalent geometry : angle 0.65369 ( 5613) SS BOND : bond 0.00348 ( 9) SS BOND : angle 1.82203 ( 18) hydrogen bonds : bond 0.02908 ( 81) hydrogen bonds : angle 5.41575 ( 216) link_NAG-ASN : bond 0.00205 ( 9) link_NAG-ASN : angle 2.25465 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7890 (mt) cc_final: 0.7489 (tm) REVERT: A 553 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8065 (m) REVERT: A 557 ASN cc_start: 0.7038 (m-40) cc_final: 0.6740 (m110) REVERT: A 567 HIS cc_start: 0.6494 (t-90) cc_final: 0.6210 (t-90) REVERT: A 639 ILE cc_start: 0.7711 (tp) cc_final: 0.7400 (pp) REVERT: A 651 LYS cc_start: 0.8429 (mmmt) cc_final: 0.7935 (mppt) REVERT: A 739 VAL cc_start: 0.6183 (p) cc_final: 0.4732 (t) REVERT: A 750 ILE cc_start: 0.5848 (OUTLIER) cc_final: 0.5612 (mp) REVERT: A 776 LEU cc_start: 0.7928 (mt) cc_final: 0.7720 (mp) REVERT: A 899 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6492 (pp20) REVERT: A 1000 ARG cc_start: 0.6315 (mpt180) cc_final: 0.5911 (tpp-160) REVERT: A 1015 GLN cc_start: 0.8311 (mm-40) cc_final: 0.8043 (mm-40) outliers start: 14 outliers final: 6 residues processed: 76 average time/residue: 0.3365 time to fit residues: 26.7990 Evaluate side-chains 72 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 993 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 0.1980 chunk 8 optimal weight: 0.0020 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 37 optimal weight: 0.0370 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 0.0970 chunk 21 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 overall best weight: 0.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS ** A 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 881 HIS A 981 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.165238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.151508 restraints weight = 7783.704| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 2.92 r_work: 0.4160 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4139 Z= 0.118 Angle : 0.670 9.578 5658 Z= 0.334 Chirality : 0.048 0.226 635 Planarity : 0.005 0.067 731 Dihedral : 7.899 59.221 725 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.56 % Allowed : 23.72 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.36), residues: 499 helix: -0.69 (0.85), residues: 35 sheet: -1.49 (0.44), residues: 139 loop : -1.25 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 872 TYR 0.010 0.001 TYR A 888 PHE 0.009 0.001 PHE A 680 TRP 0.021 0.002 TRP A 707 HIS 0.007 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 4121) covalent geometry : angle 0.65337 ( 5613) SS BOND : bond 0.00254 ( 9) SS BOND : angle 1.48170 ( 18) hydrogen bonds : bond 0.02716 ( 81) hydrogen bonds : angle 5.20164 ( 216) link_NAG-ASN : bond 0.00315 ( 9) link_NAG-ASN : angle 1.94839 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7807 (mt) cc_final: 0.7329 (tm) REVERT: A 553 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.8002 (m) REVERT: A 557 ASN cc_start: 0.6991 (m-40) cc_final: 0.6637 (m110) REVERT: A 567 HIS cc_start: 0.6400 (t-90) cc_final: 0.6075 (t-90) REVERT: A 639 ILE cc_start: 0.7671 (tp) cc_final: 0.7381 (pp) REVERT: A 651 LYS cc_start: 0.8457 (mmmt) cc_final: 0.7914 (mppt) REVERT: A 739 VAL cc_start: 0.6062 (p) cc_final: 0.4625 (t) REVERT: A 750 ILE cc_start: 0.5928 (OUTLIER) cc_final: 0.5653 (mp) REVERT: A 1000 ARG cc_start: 0.6261 (mpt180) cc_final: 0.5871 (tpp-160) REVERT: A 1015 GLN cc_start: 0.8344 (mm-40) cc_final: 0.8065 (mm-40) outliers start: 11 outliers final: 6 residues processed: 77 average time/residue: 0.3706 time to fit residues: 29.9142 Evaluate side-chains 73 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 982 ARG Chi-restraints excluded: chain A residue 993 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 HIS ** A 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.157330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.143243 restraints weight = 7848.580| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.95 r_work: 0.4116 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4139 Z= 0.171 Angle : 0.711 9.734 5658 Z= 0.350 Chirality : 0.050 0.195 635 Planarity : 0.005 0.049 731 Dihedral : 8.372 59.363 725 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 3.26 % Allowed : 22.56 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.36), residues: 499 helix: -0.94 (0.81), residues: 35 sheet: -1.40 (0.45), residues: 134 loop : -1.39 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 872 TYR 0.014 0.001 TYR A 888 PHE 0.023 0.002 PHE A 542 TRP 0.027 0.002 TRP A 707 HIS 0.008 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 4121) covalent geometry : angle 0.68763 ( 5613) SS BOND : bond 0.00392 ( 9) SS BOND : angle 1.78212 ( 18) hydrogen bonds : bond 0.03049 ( 81) hydrogen bonds : angle 5.39813 ( 216) link_NAG-ASN : bond 0.00333 ( 9) link_NAG-ASN : angle 2.37179 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1730.65 seconds wall clock time: 30 minutes 8.97 seconds (1808.97 seconds total)