Starting phenix.real_space_refine on Wed Jul 1 23:29:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wqx_32715/07_2026/7wqx_32715.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wqx_32715/07_2026/7wqx_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7wqx_32715/07_2026/7wqx_32715.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wqx_32715/07_2026/7wqx_32715.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wqx_32715/07_2026/7wqx_32715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wqx_32715/07_2026/7wqx_32715.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wqx_32715/07_2026/7wqx_32715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wqx_32715/07_2026/7wqx_32715.map" } 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-dev-6108/lib/python3.11/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 chiralities: 9 Time building chain proxies: 1.10, per 1000 atoms: 0.27 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: 0.33 Conformation dependent library (CDL) restraints added in 154.5 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: 0.13 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: 0.56 Time building geometry restraints manager: 0.47 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 - 17.55: 2288 17.55 - 35.10: 86 35.10 - 52.65: 8 52.65 - 70.21: 1 70.21 - 87.76: 2 Dihedral angle restraints: 2385 sinusoidal: 957 harmonic: 1428 Sorted by residual: dihedral pdb=" CB GLU A 674 " pdb=" CG GLU A 674 " pdb=" CD GLU A 674 " pdb=" OE1 GLU A 674 " ideal model delta sinusoidal sigma weight residual 0.00 -87.76 87.76 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" N LEU A 573 " pdb=" CA LEU A 573 " pdb=" CB LEU A 573 " pdb=" CG LEU A 573 " ideal model delta sinusoidal sigma weight residual -180.00 -121.08 -58.92 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA GLU A 587 " pdb=" CB GLU A 587 " pdb=" CG GLU A 587 " pdb=" CD GLU A 587 " ideal model delta sinusoidal sigma weight residual -60.00 -101.56 41.56 3 1.50e+01 4.44e-03 7.44e+00 ... (remaining 2382 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: 1.530 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.640 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:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 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 : 8.526 87.757 1444 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 are 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/Z covalent geometry : bond 0.00320 / 0.17 ( 4121) covalent geometry : angle 0.52609 / 0.28 ( 5613) SS BOND : bond 0.00101 / 0.05 ( 9) SS BOND : angle 0.50180 / 0.28 ( 18) hydrogen bonds : bond 0.17249 / 11.53 ( 81) hydrogen bonds : angle 6.96547 / 4.71 ( 216) link_NAG-ASN : bond 0.00235 / 0.12 ( 9) link_NAG-ASN : angle 1.13232 / 0.74 ( 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 : 0.147 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: 0.4341 time to fit residues: 48.7249 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 : 0.139 ------------------------------------------------------------------------------- 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... 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 = 0.4430 r_free = 0.4430 target = 0.162153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.147493 restraints weight = 7950.651| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 3.07 r_work: 0.4174 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4139 Z= 0.137 Angle : 0.671 12.273 5658 Z= 0.327 Chirality : 0.050 0.286 635 Planarity : 0.004 0.026 731 Dihedral : 3.785 34.506 536 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.31 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 are not related in a simple way. whole: -2.53 (0.33), residues: 499 helix: -1.43 (0.74), residues: 35 sheet: -1.64 (0.43), residues: 115 loop : -1.81 (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 0.010 0.001 PHE A 537 TRP 0.010 0.001 TRP A 707 HIS 0.003 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 4121) covalent geometry : angle 0.65261 / 0.32 ( 5613) SS BOND : bond 0.00457 / 0.24 ( 9) SS BOND : angle 2.58131 / 1.19 ( 18) hydrogen bonds : bond 0.03835 / 2.55 ( 81) hydrogen bonds : angle 5.38487 / 3.59 ( 216) link_NAG-ASN : bond 0.00231 / 0.11 ( 9) link_NAG-ASN : angle 1.19570 / 0.69 ( 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 94 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 ASP cc_start: 0.7021 (p0) cc_final: 0.6785 (p0) REVERT: A 635 TYR cc_start: 0.7608 (m-80) cc_final: 0.7281 (m-80) REVERT: A 651 LYS cc_start: 0.8394 (mmmt) cc_final: 0.8078 (mmtm) REVERT: A 750 ILE cc_start: 0.6025 (tp) cc_final: 0.5749 (mp) REVERT: A 804 TYR cc_start: 0.8066 (t80) cc_final: 0.7709 (t80) REVERT: A 845 MET cc_start: 0.6507 (mmm) cc_final: 0.6109 (mmt) REVERT: A 894 PRO cc_start: 0.8708 (Cg_endo) cc_final: 0.8496 (Cg_exo) REVERT: A 899 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6799 (pp20) REVERT: A 927 ILE cc_start: 0.7212 (mt) cc_final: 0.6878 (tt) outliers start: 14 outliers final: 6 residues processed: 87 average time/residue: 0.4671 time to fit residues: 42.1772 Evaluate side-chains 78 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.111 ------------------------------------------------------------------------------- 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: 2.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.0010 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4397 r_free = 0.4397 target = 0.159269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.144580 restraints weight = 7874.629| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 3.08 r_work: 0.4139 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.3058 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= 0.159 Angle : 0.674 9.585 5658 Z= 0.326 Chirality : 0.050 0.322 635 Planarity : 0.004 0.027 731 Dihedral : 4.327 35.132 536 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % 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 are not related in a simple way. whole: -2.27 (0.34), residues: 499 helix: -1.37 (0.73), residues: 35 sheet: -1.60 (0.44), residues: 107 loop : -1.57 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 872 TYR 0.010 0.001 TYR A 546 PHE 0.011 0.001 PHE A 542 TRP 0.014 0.002 TRP A 707 HIS 0.009 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 4121) covalent geometry : angle 0.66191 / 0.32 ( 5613) SS BOND : bond 0.00333 / 0.17 ( 9) SS BOND : angle 1.68797 / 0.80 ( 18) hydrogen bonds : bond 0.03507 / 2.29 ( 81) hydrogen bonds : angle 5.38034 / 3.51 ( 216) link_NAG-ASN : bond 0.00267 / 0.11 ( 9) link_NAG-ASN : angle 1.45516 / 0.88 ( 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 93 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.8003 (m) REVERT: A 635 TYR cc_start: 0.7632 (m-80) cc_final: 0.7299 (m-80) REVERT: A 651 LYS cc_start: 0.8420 (mmmt) cc_final: 0.7949 (mttt) REVERT: A 679 ARG cc_start: 0.6023 (mtm110) cc_final: 0.5380 (mtm110) REVERT: A 750 ILE cc_start: 0.5878 (tp) cc_final: 0.5639 (mp) REVERT: A 793 GLU cc_start: 0.5733 (OUTLIER) cc_final: 0.5505 (pm20) REVERT: A 845 MET cc_start: 0.6616 (mmm) cc_final: 0.6306 (mmt) REVERT: A 1015 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8168 (mm-40) outliers start: 13 outliers final: 2 residues processed: 90 average time/residue: 0.4515 time to fit residues: 42.2625 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 : 0.145 ------------------------------------------------------------------------------- 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 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: 0.0980 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 0.4980 chunk 21 optimal weight: 0.1980 chunk 6 optimal weight: 0.0770 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS A 647 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 = 0.4413 r_free = 0.4413 target = 0.160561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.146203 restraints weight = 7769.806| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 3.03 r_work: 0.4164 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4139 Z= 0.119 Angle : 0.639 9.497 5658 Z= 0.313 Chirality : 0.049 0.298 635 Planarity : 0.004 0.038 731 Dihedral : 4.310 33.692 536 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.79 % Allowed : 19.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.35), residues: 499 helix: -0.99 (0.79), residues: 35 sheet: -1.52 (0.43), residues: 115 loop : -1.38 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 872 TYR 0.006 0.001 TYR A 546 PHE 0.007 0.001 PHE A 542 TRP 0.024 0.002 TRP A 699 HIS 0.009 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 4121) covalent geometry : angle 0.62994 / 0.31 ( 5613) SS BOND : bond 0.00397 / 0.25 ( 9) SS BOND : angle 1.48621 / 0.76 ( 18) hydrogen bonds : bond 0.02978 / 1.93 ( 81) hydrogen bonds : angle 5.23376 / 3.38 ( 216) link_NAG-ASN : bond 0.00228 / 0.11 ( 9) link_NAG-ASN : angle 1.25728 / 0.77 ( 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 89 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 TYR cc_start: 0.7562 (m-80) cc_final: 0.7251 (m-80) REVERT: A 639 ILE cc_start: 0.7564 (tp) cc_final: 0.7235 (pp) REVERT: A 651 LYS cc_start: 0.8370 (mmmt) cc_final: 0.7933 (mttt) REVERT: A 750 ILE cc_start: 0.6028 (tp) cc_final: 0.5775 (mp) REVERT: A 813 SER cc_start: 0.8622 (m) cc_final: 0.8125 (p) REVERT: A 899 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6603 (pp20) outliers start: 12 outliers final: 3 residues processed: 86 average time/residue: 0.4458 time to fit residues: 39.9470 Evaluate side-chains 77 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 899 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: 0.5980 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.0470 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.0670 chunk 7 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 636 HIS A 647 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.165490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.151487 restraints weight = 7834.569| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 2.99 r_work: 0.4164 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.3448 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= 0.117 Angle : 0.631 9.532 5658 Z= 0.306 Chirality : 0.049 0.294 635 Planarity : 0.004 0.031 731 Dihedral : 4.286 33.765 536 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.02 % Allowed : 18.84 % Favored : 78.14 % 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 are not related in a simple way. whole: -1.95 (0.35), residues: 499 helix: -0.77 (0.83), residues: 35 sheet: -1.29 (0.47), residues: 104 loop : -1.42 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 872 TYR 0.014 0.001 TYR A 888 PHE 0.007 0.001 PHE A 568 TRP 0.026 0.002 TRP A 699 HIS 0.009 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 4121) covalent geometry : angle 0.62215 / 0.30 ( 5613) SS BOND : bond 0.00244 / 0.13 ( 9) SS BOND : angle 1.48662 / 0.79 ( 18) hydrogen bonds : bond 0.03053 / 1.95 ( 81) hydrogen bonds : angle 5.06167 / 3.28 ( 216) link_NAG-ASN : bond 0.00222 / 0.10 ( 9) link_NAG-ASN : angle 1.23610 / 0.77 ( 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 84 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 619 ASN cc_start: 0.6544 (p0) cc_final: 0.5993 (p0) REVERT: A 639 ILE cc_start: 0.7578 (tp) cc_final: 0.7261 (pp) REVERT: A 651 LYS cc_start: 0.8374 (mmmt) cc_final: 0.7941 (mttt) REVERT: A 750 ILE cc_start: 0.6000 (OUTLIER) cc_final: 0.5745 (mp) REVERT: A 774 LYS cc_start: 0.6937 (mttp) cc_final: 0.6553 (mptp) REVERT: A 793 GLU cc_start: 0.5750 (OUTLIER) cc_final: 0.5541 (pm20) REVERT: A 813 SER cc_start: 0.8585 (m) cc_final: 0.8117 (p) REVERT: A 899 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6596 (pp20) REVERT: A 955 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8502 (tp) outliers start: 13 outliers final: 4 residues processed: 82 average time/residue: 0.3754 time to fit residues: 32.2253 Evaluate side-chains 75 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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 955 ILE 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: 0.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.0060 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 0.0670 overall best weight: 0.2492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 636 HIS A 647 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.161525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.147735 restraints weight = 7942.911| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 2.90 r_work: 0.4176 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4139 Z= 0.123 Angle : 0.657 9.503 5658 Z= 0.325 Chirality : 0.050 0.285 635 Planarity : 0.004 0.033 731 Dihedral : 4.348 33.957 536 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.49 % Allowed : 17.67 % Favored : 78.84 % 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 are not related in a simple way. whole: -1.80 (0.35), residues: 499 helix: -0.58 (0.86), residues: 35 sheet: -1.04 (0.45), residues: 115 loop : -1.37 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1000 TYR 0.007 0.001 TYR A 948 PHE 0.016 0.001 PHE A 542 TRP 0.014 0.001 TRP A 707 HIS 0.009 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 4121) covalent geometry : angle 0.64680 / 0.32 ( 5613) SS BOND : bond 0.00242 / 0.13 ( 9) SS BOND : angle 1.70661 / 0.96 ( 18) hydrogen bonds : bond 0.02783 / 1.80 ( 81) hydrogen bonds : angle 4.93535 / 3.18 ( 216) link_NAG-ASN : bond 0.00265 / 0.13 ( 9) link_NAG-ASN : angle 1.20889 / 0.76 ( 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 89 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 553 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8066 (m) REVERT: A 557 ASN cc_start: 0.6907 (m-40) cc_final: 0.6309 (p0) REVERT: A 639 ILE cc_start: 0.7573 (tp) cc_final: 0.7263 (pp) REVERT: A 651 LYS cc_start: 0.8385 (mmmt) cc_final: 0.7998 (mmtm) REVERT: A 750 ILE cc_start: 0.6012 (OUTLIER) cc_final: 0.5762 (mp) REVERT: A 793 GLU cc_start: 0.5755 (OUTLIER) cc_final: 0.5540 (pm20) REVERT: A 899 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6666 (pp20) REVERT: A 955 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8483 (tp) outliers start: 15 outliers final: 3 residues processed: 84 average time/residue: 0.4073 time to fit residues: 35.7549 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 : 0.171 ------------------------------------------------------------------------------- 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 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 955 ILE 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: 0.8980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.0770 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 ASN A 636 HIS ** A 667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN ** A 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN A 929 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.156890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.142033 restraints weight = 7905.558| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 3.08 r_work: 0.4104 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4139 Z= 0.223 Angle : 0.782 9.861 5658 Z= 0.381 Chirality : 0.054 0.356 635 Planarity : 0.005 0.046 731 Dihedral : 4.901 34.624 536 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 2.33 % Allowed : 20.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.35), residues: 499 helix: -1.28 (0.75), residues: 35 sheet: -1.38 (0.44), residues: 125 loop : -1.46 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 872 TYR 0.012 0.001 TYR A 546 PHE 0.020 0.002 PHE A 680 TRP 0.026 0.002 TRP A 707 HIS 0.009 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 ( 4121) covalent geometry : angle 0.76647 / 0.38 ( 5613) SS BOND : bond 0.00410 / 0.22 ( 9) SS BOND : angle 1.89817 / 1.02 ( 18) hydrogen bonds : bond 0.03611 / 2.32 ( 81) hydrogen bonds : angle 5.68781 / 3.71 ( 216) link_NAG-ASN : bond 0.00456 / 0.20 ( 9) link_NAG-ASN : angle 1.92064 / 1.23 ( 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 88 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.7752 (tp) cc_final: 0.7400 (pp) REVERT: A 651 LYS cc_start: 0.8521 (mmmt) cc_final: 0.7961 (mppt) REVERT: A 750 ILE cc_start: 0.5817 (OUTLIER) cc_final: 0.5605 (mp) REVERT: A 776 LEU cc_start: 0.7995 (mt) cc_final: 0.7790 (mp) REVERT: A 813 SER cc_start: 0.8649 (m) cc_final: 0.8131 (p) REVERT: A 1015 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8091 (mm-40) outliers start: 10 outliers final: 4 residues processed: 85 average time/residue: 0.3934 time to fit residues: 35.0141 Evaluate side-chains 75 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 701 THR Chi-restraints excluded: chain A residue 750 ILE 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: 0.7980 chunk 39 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 44 optimal weight: 0.0980 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4371 r_free = 0.4371 target = 0.157538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.142996 restraints weight = 7821.422| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 3.01 r_work: 0.4115 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.4350 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= 0.169 Angle : 0.716 9.653 5658 Z= 0.349 Chirality : 0.052 0.322 635 Planarity : 0.004 0.044 731 Dihedral : 4.849 35.804 536 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.56 % Allowed : 22.33 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.35), residues: 499 helix: -1.17 (0.80), residues: 35 sheet: -1.25 (0.46), residues: 124 loop : -1.42 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 872 TYR 0.013 0.001 TYR A 888 PHE 0.017 0.002 PHE A 542 TRP 0.018 0.002 TRP A 707 HIS 0.009 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 4121) covalent geometry : angle 0.70367 / 0.35 ( 5613) SS BOND : bond 0.00321 / 0.17 ( 9) SS BOND : angle 1.63847 / 0.87 ( 18) hydrogen bonds : bond 0.03177 / 2.08 ( 81) hydrogen bonds : angle 5.53108 / 3.60 ( 216) link_NAG-ASN : bond 0.00258 / 0.11 ( 9) link_NAG-ASN : angle 1.67802 / 1.14 ( 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 82 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 557 ASN cc_start: 0.7006 (m110) cc_final: 0.6707 (m110) REVERT: A 612 MET cc_start: 0.8089 (ttp) cc_final: 0.7794 (mtp) REVERT: A 639 ILE cc_start: 0.7826 (tp) cc_final: 0.7510 (pp) REVERT: A 651 LYS cc_start: 0.8455 (mmmt) cc_final: 0.7958 (mppt) REVERT: A 750 ILE cc_start: 0.5820 (OUTLIER) cc_final: 0.5597 (mp) REVERT: A 776 LEU cc_start: 0.8019 (mt) cc_final: 0.7794 (mp) REVERT: A 813 SER cc_start: 0.8649 (m) cc_final: 0.8109 (p) REVERT: A 947 GLU cc_start: 0.7862 (pm20) cc_final: 0.7652 (pm20) REVERT: A 1015 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8137 (mm-40) outliers start: 11 outliers final: 6 residues processed: 79 average time/residue: 0.3628 time to fit residues: 30.0071 Evaluate side-chains 78 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.125 ------------------------------------------------------------------------------- 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 701 THR Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 923 THR 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: 2.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4363 r_free = 0.4363 target = 0.156890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.142066 restraints weight = 7908.040| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 3.07 r_work: 0.4106 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4139 Z= 0.178 Angle : 0.744 9.737 5658 Z= 0.362 Chirality : 0.052 0.323 635 Planarity : 0.005 0.073 731 Dihedral : 5.023 35.721 536 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.56 % Allowed : 23.49 % Favored : 73.95 % 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 are not related in a simple way. whole: -2.11 (0.35), residues: 499 helix: -1.24 (0.79), residues: 35 sheet: -1.23 (0.46), residues: 125 loop : -1.54 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 872 TYR 0.016 0.001 TYR A 948 PHE 0.020 0.002 PHE A 542 TRP 0.022 0.002 TRP A 707 HIS 0.008 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 4121) covalent geometry : angle 0.73165 / 0.36 ( 5613) SS BOND : bond 0.00354 / 0.19 ( 9) SS BOND : angle 1.63492 / 0.87 ( 18) hydrogen bonds : bond 0.03278 / 2.17 ( 81) hydrogen bonds : angle 5.59882 / 3.63 ( 216) link_NAG-ASN : bond 0.00294 / 0.13 ( 9) link_NAG-ASN : angle 1.74594 / 1.20 ( 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 77 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 557 ASN cc_start: 0.7015 (m110) cc_final: 0.6726 (m110) REVERT: A 612 MET cc_start: 0.8187 (ttp) cc_final: 0.7927 (mtp) REVERT: A 639 ILE cc_start: 0.7821 (tp) cc_final: 0.7507 (pp) REVERT: A 651 LYS cc_start: 0.8483 (mmmt) cc_final: 0.7965 (mppt) REVERT: A 723 SER cc_start: 0.8376 (t) cc_final: 0.8101 (p) REVERT: A 739 VAL cc_start: 0.6362 (p) cc_final: 0.4933 (t) REVERT: A 750 ILE cc_start: 0.5867 (OUTLIER) cc_final: 0.5623 (mp) REVERT: A 776 LEU cc_start: 0.8010 (mt) cc_final: 0.7778 (mp) REVERT: A 813 SER cc_start: 0.8707 (m) cc_final: 0.8158 (p) REVERT: A 899 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6526 (pp20) REVERT: A 947 GLU cc_start: 0.7840 (pm20) cc_final: 0.7606 (pm20) REVERT: A 1000 ARG cc_start: 0.6290 (mpt180) cc_final: 0.5875 (tpp-160) REVERT: A 1015 GLN cc_start: 0.8388 (mm-40) cc_final: 0.8139 (mm-40) outliers start: 11 outliers final: 8 residues processed: 74 average time/residue: 0.3610 time to fit residues: 27.9950 Evaluate side-chains 72 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 690 LEU 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 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: 0.0470 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 29 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.157849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.143310 restraints weight = 7911.176| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 3.02 r_work: 0.4119 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.4534 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= 0.151 Angle : 0.731 9.593 5658 Z= 0.355 Chirality : 0.052 0.308 635 Planarity : 0.005 0.072 731 Dihedral : 5.051 35.819 536 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.09 % Allowed : 24.88 % Favored : 73.02 % 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 are not related in a simple way. whole: -2.03 (0.36), residues: 499 helix: -1.18 (0.79), residues: 35 sheet: -1.21 (0.46), residues: 130 loop : -1.47 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 872 TYR 0.019 0.002 TYR A 948 PHE 0.017 0.002 PHE A 542 TRP 0.032 0.002 TRP A 699 HIS 0.008 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 4121) covalent geometry : angle 0.71938 / 0.35 ( 5613) SS BOND : bond 0.00321 / 0.17 ( 9) SS BOND : angle 1.57928 / 0.84 ( 18) hydrogen bonds : bond 0.03196 / 2.13 ( 81) hydrogen bonds : angle 5.52313 / 3.59 ( 216) link_NAG-ASN : bond 0.00213 / 0.10 ( 9) link_NAG-ASN : angle 1.62703 / 1.12 ( 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 73 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 557 ASN cc_start: 0.7016 (m110) cc_final: 0.6710 (m110) REVERT: A 612 MET cc_start: 0.8174 (ttp) cc_final: 0.7914 (mtp) REVERT: A 639 ILE cc_start: 0.7810 (tp) cc_final: 0.7492 (pp) REVERT: A 651 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8000 (mppt) REVERT: A 691 VAL cc_start: 0.6303 (p) cc_final: 0.6025 (t) REVERT: A 723 SER cc_start: 0.8336 (t) cc_final: 0.8053 (p) REVERT: A 750 ILE cc_start: 0.5829 (OUTLIER) cc_final: 0.5601 (mp) REVERT: A 776 LEU cc_start: 0.7996 (mt) cc_final: 0.7769 (mp) REVERT: A 813 SER cc_start: 0.8678 (m) cc_final: 0.8137 (p) REVERT: A 899 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6621 (pp20) REVERT: A 947 GLU cc_start: 0.7853 (pm20) cc_final: 0.7632 (pm20) REVERT: A 1000 ARG cc_start: 0.6276 (mpt180) cc_final: 0.5870 (tpp-160) REVERT: A 1015 GLN cc_start: 0.8379 (mm-40) cc_final: 0.8130 (mm-40) outliers start: 9 outliers final: 5 residues processed: 70 average time/residue: 0.3554 time to fit residues: 26.1502 Evaluate side-chains 67 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.108 ------------------------------------------------------------------------------- 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 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 47 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 0.0170 chunk 5 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4369 r_free = 0.4369 target = 0.157547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.143047 restraints weight = 7892.263| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 3.02 r_work: 0.4114 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4139 Z= 0.164 Angle : 0.738 9.688 5658 Z= 0.357 Chirality : 0.052 0.312 635 Planarity : 0.005 0.050 731 Dihedral : 5.006 36.114 536 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 2.33 % Allowed : 24.42 % Favored : 73.26 % 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 are not related in a simple way. whole: -2.06 (0.36), residues: 499 helix: -1.25 (0.79), residues: 35 sheet: -1.04 (0.49), residues: 118 loop : -1.58 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 872 TYR 0.016 0.002 TYR A 888 PHE 0.015 0.002 PHE A 542 TRP 0.025 0.002 TRP A 707 HIS 0.009 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 4121) covalent geometry : angle 0.72590 / 0.35 ( 5613) SS BOND : bond 0.00340 / 0.18 ( 9) SS BOND : angle 1.52782 / 0.79 ( 18) hydrogen bonds : bond 0.03262 / 2.14 ( 81) hydrogen bonds : angle 5.55339 / 3.63 ( 216) link_NAG-ASN : bond 0.00259 / 0.11 ( 9) link_NAG-ASN : angle 1.69838 / 1.17 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1754.10 seconds wall clock time: 30 minutes 35.62 seconds (1835.62 seconds total)