Starting phenix.real_space_refine on Wed Jun 4 20:54:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wqx_32715/06_2025/7wqx_32715.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wqx_32715/06_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_32715/06_2025/7wqx_32715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wqx_32715/06_2025/7wqx_32715.map" model { file = "/net/cci-nas-00/data/ceres_data/7wqx_32715/06_2025/7wqx_32715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wqx_32715/06_2025/7wqx_32715.cif" } resolution = 2.7 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= 0.011 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 3.04, per 1000 atoms: 0.76 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: 0.86 Conformation dependent library (CDL) restraints added in 549.9 milliseconds 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: 0.51 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: 1.14 Time building geometry restraints manager: 1.03 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.460 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.010 ------------------------------------------------------------------------------- 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 (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: -3.61 (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 TRP 0.004 0.001 TRP A 699 HIS 0.001 0.000 HIS A 825 PHE 0.005 0.001 PHE A 693 TYR 0.004 0.000 TYR A 546 ARG 0.001 0.000 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 9) link_NAG-ASN : angle 1.13232 ( 27) hydrogen bonds : bond 0.17249 ( 81) hydrogen bonds : angle 6.96547 ( 216) SS BOND : bond 0.00101 ( 9) SS BOND : angle 0.50180 ( 18) covalent geometry : bond 0.00320 ( 4121) covalent geometry : angle 0.52609 ( 5613) *********************** 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 : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7737 (mt) cc_final: 0.7446 (tm) REVERT: A 635 TYR cc_start: 0.7168 (m-80) cc_final: 0.6718 (m-80) REVERT: A 651 LYS cc_start: 0.8311 (mmmt) cc_final: 0.7958 (mppt) REVERT: A 927 ILE cc_start: 0.6968 (mt) cc_final: 0.6643 (mt) outliers start: 11 outliers final: 1 residues processed: 108 average time/residue: 0.9373 time to fit residues: 105.3712 Evaluate side-chains 77 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 42 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.0030 chunk 25 optimal weight: 0.0470 chunk 20 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.4088 ------------------------------------------------------------------------------- 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 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 = 0.4435 r_free = 0.4435 target = 0.162529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.147986 restraints weight = 7786.075| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 3.02 r_work: 0.4185 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4139 Z= 0.136 Angle : 0.688 11.958 5658 Z= 0.330 Chirality : 0.049 0.201 635 Planarity : 0.004 0.026 731 Dihedral : 11.321 90.503 725 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.43 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.33), residues: 499 helix: -1.21 (0.77), residues: 35 sheet: -1.62 (0.42), residues: 116 loop : -1.83 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 707 HIS 0.003 0.001 HIS A 844 PHE 0.010 0.001 PHE A 537 TYR 0.010 0.001 TYR A 804 ARG 0.007 0.001 ARG A 872 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 9) link_NAG-ASN : angle 1.41998 ( 27) hydrogen bonds : bond 0.03648 ( 81) hydrogen bonds : angle 5.33263 ( 216) SS BOND : bond 0.00945 ( 9) SS BOND : angle 2.40344 ( 18) covalent geometry : bond 0.00297 ( 4121) covalent geometry : angle 0.66953 ( 5613) *********************** 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 94 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 ASP cc_start: 0.6964 (p0) cc_final: 0.6718 (p0) REVERT: A 635 TYR cc_start: 0.7574 (m-80) cc_final: 0.7271 (m-80) REVERT: A 651 LYS cc_start: 0.8351 (mmmt) cc_final: 0.8071 (mmtm) REVERT: A 750 ILE cc_start: 0.6010 (tp) cc_final: 0.5740 (mp) REVERT: A 804 TYR cc_start: 0.8084 (t80) cc_final: 0.7639 (t80) REVERT: A 845 MET cc_start: 0.6494 (mmm) cc_final: 0.6103 (mmt) REVERT: A 894 PRO cc_start: 0.8698 (Cg_endo) cc_final: 0.8446 (Cg_exo) REVERT: A 899 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6735 (pp20) REVERT: A 927 ILE cc_start: 0.7212 (mt) cc_final: 0.6860 (tt) outliers start: 14 outliers final: 6 residues processed: 87 average time/residue: 0.9622 time to fit residues: 87.1125 Evaluate side-chains 79 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 19 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 12 optimal weight: 0.0170 chunk 42 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4396 r_free = 0.4396 target = 0.159219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.144677 restraints weight = 7785.012| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 3.05 r_work: 0.4142 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4139 Z= 0.160 Angle : 0.698 10.679 5658 Z= 0.330 Chirality : 0.048 0.193 635 Planarity : 0.004 0.027 731 Dihedral : 8.876 57.984 725 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.49 % Allowed : 16.28 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.34), residues: 499 helix: -0.89 (0.81), residues: 35 sheet: -1.51 (0.44), residues: 110 loop : -1.62 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 707 HIS 0.009 0.001 HIS A 636 PHE 0.011 0.001 PHE A 542 TYR 0.009 0.001 TYR A 546 ARG 0.009 0.001 ARG A 872 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 9) link_NAG-ASN : angle 2.36092 ( 27) hydrogen bonds : bond 0.03448 ( 81) hydrogen bonds : angle 5.31272 ( 216) SS BOND : bond 0.00331 ( 9) SS BOND : angle 1.68905 ( 18) covalent geometry : bond 0.00354 ( 4121) covalent geometry : angle 0.67464 ( 5613) *********************** 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 92 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 VAL cc_start: 0.8401 (OUTLIER) cc_final: 0.8067 (m) REVERT: A 635 TYR cc_start: 0.7633 (m-80) cc_final: 0.7265 (m-80) REVERT: A 651 LYS cc_start: 0.8397 (mmmt) cc_final: 0.7970 (mttt) REVERT: A 750 ILE cc_start: 0.5869 (tp) cc_final: 0.5635 (mp) REVERT: A 793 GLU cc_start: 0.5712 (OUTLIER) cc_final: 0.5486 (pm20) REVERT: A 845 MET cc_start: 0.6607 (mmm) cc_final: 0.6236 (mmt) REVERT: A 927 ILE cc_start: 0.7476 (mt) cc_final: 0.7103 (tt) outliers start: 15 outliers final: 3 residues processed: 86 average time/residue: 1.3591 time to fit residues: 120.9794 Evaluate side-chains 80 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 793 GLU Chi-restraints excluded: chain A residue 836 LYS 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 49 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 44 optimal weight: 0.0470 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.158539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.143952 restraints weight = 7725.231| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 3.02 r_work: 0.4131 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4139 Z= 0.160 Angle : 0.671 9.710 5658 Z= 0.323 Chirality : 0.048 0.192 635 Planarity : 0.004 0.043 731 Dihedral : 8.298 58.523 725 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 3.72 % Allowed : 17.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.35), residues: 499 helix: -0.70 (0.86), residues: 35 sheet: -1.47 (0.43), residues: 118 loop : -1.50 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 699 HIS 0.008 0.001 HIS A 636 PHE 0.008 0.001 PHE A 680 TYR 0.009 0.001 TYR A 804 ARG 0.009 0.001 ARG A 872 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 9) link_NAG-ASN : angle 2.30558 ( 27) hydrogen bonds : bond 0.03208 ( 81) hydrogen bonds : angle 5.26979 ( 216) SS BOND : bond 0.00424 ( 9) SS BOND : angle 1.71405 ( 18) covalent geometry : bond 0.00362 ( 4121) covalent geometry : angle 0.64757 ( 5613) *********************** 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 90 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 553 VAL cc_start: 0.8367 (t) cc_final: 0.8030 (m) REVERT: A 635 TYR cc_start: 0.7618 (m-80) cc_final: 0.7271 (m-80) REVERT: A 639 ILE cc_start: 0.7639 (tp) cc_final: 0.7284 (pp) REVERT: A 651 LYS cc_start: 0.8415 (mmmt) cc_final: 0.7917 (mppt) REVERT: A 750 ILE cc_start: 0.5886 (tp) cc_final: 0.5650 (mp) REVERT: A 793 GLU cc_start: 0.5835 (OUTLIER) cc_final: 0.5625 (pm20) REVERT: A 813 SER cc_start: 0.8662 (m) cc_final: 0.8161 (p) REVERT: A 845 MET cc_start: 0.6638 (mmm) cc_final: 0.6305 (mmt) REVERT: A 899 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6698 (pp20) REVERT: A 955 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8514 (tp) REVERT: A 1000 ARG cc_start: 0.6557 (mmm160) cc_final: 0.6351 (mpt180) outliers start: 16 outliers final: 4 residues processed: 88 average time/residue: 1.1045 time to fit residues: 101.0191 Evaluate side-chains 76 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 836 LYS Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 955 ILE 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 35 optimal weight: 0.6980 chunk 21 optimal weight: 0.0770 chunk 25 optimal weight: 3.9990 chunk 13 optimal weight: 0.0030 chunk 2 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 0.4948 ------------------------------------------------------------------------------- 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 = 0.4387 r_free = 0.4387 target = 0.158868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.144259 restraints weight = 7935.625| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 3.10 r_work: 0.4128 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4139 Z= 0.137 Angle : 0.652 9.713 5658 Z= 0.313 Chirality : 0.048 0.201 635 Planarity : 0.004 0.031 731 Dihedral : 8.222 58.974 725 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.56 % Allowed : 19.53 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.36), residues: 499 helix: -0.51 (0.89), residues: 35 sheet: -1.64 (0.41), residues: 137 loop : -1.35 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 699 HIS 0.009 0.001 HIS A 636 PHE 0.016 0.001 PHE A 680 TYR 0.013 0.001 TYR A 888 ARG 0.009 0.001 ARG A 872 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 9) link_NAG-ASN : angle 2.20610 ( 27) hydrogen bonds : bond 0.03021 ( 81) hydrogen bonds : angle 5.17381 ( 216) SS BOND : bond 0.00461 ( 9) SS BOND : angle 1.99622 ( 18) covalent geometry : bond 0.00311 ( 4121) covalent geometry : angle 0.62646 ( 5613) *********************** 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 82 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 557 ASN cc_start: 0.7188 (m110) cc_final: 0.6900 (m110) REVERT: A 635 TYR cc_start: 0.7601 (m-80) cc_final: 0.7385 (m-80) REVERT: A 639 ILE cc_start: 0.7616 (tp) cc_final: 0.7293 (pp) REVERT: A 651 LYS cc_start: 0.8408 (mmmt) cc_final: 0.7904 (mppt) REVERT: A 750 ILE cc_start: 0.5876 (OUTLIER) cc_final: 0.5652 (mp) REVERT: A 793 GLU cc_start: 0.5840 (OUTLIER) cc_final: 0.5633 (pm20) REVERT: A 813 SER cc_start: 0.8658 (m) cc_final: 0.8147 (p) REVERT: A 899 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6506 (pp20) outliers start: 11 outliers final: 4 residues processed: 80 average time/residue: 1.1058 time to fit residues: 94.2901 Evaluate side-chains 81 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 701 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 793 GLU 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 34 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 chunk 49 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.158715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.144316 restraints weight = 7782.580| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 3.04 r_work: 0.4137 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4139 Z= 0.143 Angle : 0.671 9.717 5658 Z= 0.323 Chirality : 0.048 0.201 635 Planarity : 0.004 0.033 731 Dihedral : 8.194 58.920 725 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.26 % Allowed : 19.07 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.36), residues: 499 helix: -0.48 (0.90), residues: 35 sheet: -1.60 (0.41), residues: 139 loop : -1.36 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 699 HIS 0.008 0.001 HIS A 636 PHE 0.009 0.001 PHE A 680 TYR 0.008 0.001 TYR A 546 ARG 0.011 0.001 ARG A 872 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 9) link_NAG-ASN : angle 2.22899 ( 27) hydrogen bonds : bond 0.02985 ( 81) hydrogen bonds : angle 5.18311 ( 216) SS BOND : bond 0.00290 ( 9) SS BOND : angle 1.67447 ( 18) covalent geometry : bond 0.00324 ( 4121) covalent geometry : angle 0.64856 ( 5613) *********************** 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 86 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7904 (mt) cc_final: 0.7512 (tm) REVERT: A 557 ASN cc_start: 0.7179 (m110) cc_final: 0.6765 (m110) REVERT: A 639 ILE cc_start: 0.7626 (tp) cc_final: 0.7313 (pp) REVERT: A 651 LYS cc_start: 0.8420 (mmmt) cc_final: 0.7912 (mppt) REVERT: A 813 SER cc_start: 0.8633 (m) cc_final: 0.8135 (p) REVERT: A 899 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6493 (pp20) outliers start: 14 outliers final: 6 residues processed: 82 average time/residue: 0.8264 time to fit residues: 71.1469 Evaluate side-chains 76 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 742 ASN Chi-restraints excluded: chain A residue 899 GLU 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 17 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 15 optimal weight: 20.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 929 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.157495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.142802 restraints weight = 7848.036| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 3.07 r_work: 0.4118 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4139 Z= 0.165 Angle : 0.691 9.746 5658 Z= 0.334 Chirality : 0.049 0.195 635 Planarity : 0.004 0.046 731 Dihedral : 8.315 58.789 725 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 2.56 % Allowed : 20.47 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.35), residues: 499 helix: -0.56 (0.89), residues: 35 sheet: -1.52 (0.41), residues: 137 loop : -1.40 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 707 HIS 0.008 0.001 HIS A 636 PHE 0.009 0.001 PHE A1017 TYR 0.013 0.001 TYR A 888 ARG 0.011 0.001 ARG A 872 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 9) link_NAG-ASN : angle 2.38249 ( 27) hydrogen bonds : bond 0.02970 ( 81) hydrogen bonds : angle 5.32502 ( 216) SS BOND : bond 0.00317 ( 9) SS BOND : angle 1.66371 ( 18) covalent geometry : bond 0.00376 ( 4121) covalent geometry : angle 0.66735 ( 5613) *********************** 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 82 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7928 (mt) cc_final: 0.7538 (tm) REVERT: A 557 ASN cc_start: 0.7073 (m110) cc_final: 0.6645 (m110) REVERT: A 639 ILE cc_start: 0.7681 (tp) cc_final: 0.7370 (pp) REVERT: A 651 LYS cc_start: 0.8460 (mmmt) cc_final: 0.7946 (mppt) REVERT: A 833 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6730 (tm-30) REVERT: A 899 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6523 (pp20) REVERT: A 1015 GLN cc_start: 0.8455 (mm110) cc_final: 0.8185 (mm-40) outliers start: 11 outliers final: 5 residues processed: 80 average time/residue: 0.9046 time to fit residues: 75.6568 Evaluate side-chains 71 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 833 GLU Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 923 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 15 optimal weight: 0.0770 chunk 4 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.158125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.143700 restraints weight = 7696.752| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.99 r_work: 0.4130 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4139 Z= 0.137 Angle : 0.686 9.669 5658 Z= 0.332 Chirality : 0.049 0.201 635 Planarity : 0.004 0.038 731 Dihedral : 8.043 59.824 723 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.33 % Allowed : 21.16 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.36), residues: 499 helix: -0.39 (0.90), residues: 35 sheet: -1.32 (0.44), residues: 118 loop : -1.42 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 707 HIS 0.008 0.001 HIS A 636 PHE 0.009 0.001 PHE A 542 TYR 0.008 0.001 TYR A 546 ARG 0.012 0.001 ARG A 872 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 9) link_NAG-ASN : angle 2.20328 ( 27) hydrogen bonds : bond 0.02890 ( 81) hydrogen bonds : angle 5.32900 ( 216) SS BOND : bond 0.00282 ( 9) SS BOND : angle 1.49946 ( 18) covalent geometry : bond 0.00316 ( 4121) covalent geometry : angle 0.66569 ( 5613) *********************** 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 74 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7881 (mt) cc_final: 0.7486 (tm) REVERT: A 557 ASN cc_start: 0.7066 (m110) cc_final: 0.6701 (m110) REVERT: A 639 ILE cc_start: 0.7690 (tp) cc_final: 0.7385 (pp) REVERT: A 651 LYS cc_start: 0.8438 (mmmt) cc_final: 0.7940 (mppt) REVERT: A 750 ILE cc_start: 0.5958 (OUTLIER) cc_final: 0.5631 (mp) REVERT: A 899 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6592 (pp20) outliers start: 10 outliers final: 5 residues processed: 70 average time/residue: 0.8116 time to fit residues: 59.7488 Evaluate side-chains 72 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 793 GLU Chi-restraints excluded: chain A residue 899 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.1980 chunk 21 optimal weight: 0.0370 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.157032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.142337 restraints weight = 7852.155| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 3.07 r_work: 0.4113 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4139 Z= 0.163 Angle : 0.721 9.710 5658 Z= 0.348 Chirality : 0.049 0.193 635 Planarity : 0.005 0.067 731 Dihedral : 8.154 59.542 723 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 3.49 % Allowed : 21.16 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.36), residues: 499 helix: -0.55 (0.89), residues: 35 sheet: -1.44 (0.45), residues: 121 loop : -1.48 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 707 HIS 0.008 0.001 HIS A 636 PHE 0.012 0.001 PHE A 542 TYR 0.009 0.001 TYR A 546 ARG 0.018 0.001 ARG A 872 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 9) link_NAG-ASN : angle 2.43132 ( 27) hydrogen bonds : bond 0.03041 ( 81) hydrogen bonds : angle 5.57519 ( 216) SS BOND : bond 0.00327 ( 9) SS BOND : angle 1.49408 ( 18) covalent geometry : bond 0.00371 ( 4121) covalent geometry : angle 0.69927 ( 5613) *********************** 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 88 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7938 (mt) cc_final: 0.7462 (tm) REVERT: A 557 ASN cc_start: 0.7026 (m110) cc_final: 0.6655 (m110) REVERT: A 612 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8115 (mtm) REVERT: A 639 ILE cc_start: 0.7758 (tp) cc_final: 0.7457 (pp) REVERT: A 651 LYS cc_start: 0.8458 (mmmt) cc_final: 0.7955 (mppt) REVERT: A 739 VAL cc_start: 0.6212 (p) cc_final: 0.4758 (t) REVERT: A 750 ILE cc_start: 0.5925 (OUTLIER) cc_final: 0.5617 (mp) REVERT: A 813 SER cc_start: 0.8630 (m) cc_final: 0.8139 (p) REVERT: A 899 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6601 (pp20) REVERT: A 1015 GLN cc_start: 0.8419 (mm110) cc_final: 0.8166 (mm110) outliers start: 15 outliers final: 7 residues processed: 83 average time/residue: 0.9866 time to fit residues: 85.2476 Evaluate side-chains 77 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 612 MET 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 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 33 optimal weight: 0.9990 chunk 22 optimal weight: 0.0050 chunk 25 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.0010 chunk 7 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 0.0030 chunk 48 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.2410 ------------------------------------------------------------------------------- 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 881 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.159326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.144831 restraints weight = 7857.725| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 3.06 r_work: 0.4145 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4139 Z= 0.121 Angle : 0.679 9.580 5658 Z= 0.333 Chirality : 0.049 0.209 635 Planarity : 0.005 0.067 731 Dihedral : 7.811 59.327 723 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.56 % Allowed : 23.02 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.36), residues: 499 helix: -0.32 (0.90), residues: 35 sheet: -1.14 (0.46), residues: 116 loop : -1.38 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 699 HIS 0.011 0.001 HIS A 636 PHE 0.010 0.001 PHE A 542 TYR 0.007 0.001 TYR A 546 ARG 0.019 0.001 ARG A 872 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 9) link_NAG-ASN : angle 2.03107 ( 27) hydrogen bonds : bond 0.02691 ( 81) hydrogen bonds : angle 5.33068 ( 216) SS BOND : bond 0.00264 ( 9) SS BOND : angle 1.28058 ( 18) covalent geometry : bond 0.00274 ( 4121) covalent geometry : angle 0.66303 ( 5613) ********************** 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 80 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 LEU cc_start: 0.7859 (mt) cc_final: 0.7426 (tm) REVERT: A 557 ASN cc_start: 0.7010 (m110) cc_final: 0.6653 (m110) REVERT: A 639 ILE cc_start: 0.7786 (tp) cc_final: 0.7512 (pp) REVERT: A 651 LYS cc_start: 0.8437 (mmmt) cc_final: 0.7933 (mppt) REVERT: A 739 VAL cc_start: 0.6126 (p) cc_final: 0.4687 (t) REVERT: A 750 ILE cc_start: 0.5913 (OUTLIER) cc_final: 0.5609 (mp) REVERT: A 899 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6650 (pp20) REVERT: A 947 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7532 (pm20) REVERT: A 1000 ARG cc_start: 0.6270 (mpt180) cc_final: 0.5866 (tpp-160) REVERT: A 1015 GLN cc_start: 0.8410 (mm110) cc_final: 0.8134 (mm110) outliers start: 11 outliers final: 6 residues processed: 76 average time/residue: 1.3484 time to fit residues: 109.1035 Evaluate side-chains 73 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 947 GLU 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 16 optimal weight: 0.0670 chunk 43 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 27 optimal weight: 0.0060 chunk 44 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 overall best weight: 0.4734 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.158002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.143565 restraints weight = 7712.912| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.98 r_work: 0.4128 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.4490 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= 0.144 Angle : 0.716 9.674 5658 Z= 0.348 Chirality : 0.049 0.202 635 Planarity : 0.005 0.067 731 Dihedral : 7.991 59.739 723 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 3.02 % Allowed : 22.56 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.36), residues: 499 helix: -0.35 (0.89), residues: 35 sheet: -1.09 (0.47), residues: 116 loop : -1.39 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 707 HIS 0.008 0.001 HIS A 636 PHE 0.011 0.001 PHE A 542 TYR 0.009 0.001 TYR A 804 ARG 0.020 0.001 ARG A 872 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 9) link_NAG-ASN : angle 2.22636 ( 27) hydrogen bonds : bond 0.02915 ( 81) hydrogen bonds : angle 5.38690 ( 216) SS BOND : bond 0.00303 ( 9) SS BOND : angle 1.51639 ( 18) covalent geometry : bond 0.00334 ( 4121) covalent geometry : angle 0.69671 ( 5613) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4246.37 seconds wall clock time: 76 minutes 35.32 seconds (4595.32 seconds total)