Starting phenix.real_space_refine on Wed Jul 1 23:39:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lkh_23408/07_2026/7lkh_23408.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lkh_23408/07_2026/7lkh_23408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lkh_23408/07_2026/7lkh_23408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lkh_23408/07_2026/7lkh_23408.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lkh_23408/07_2026/7lkh_23408.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lkh_23408/07_2026/7lkh_23408.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lkh_23408/07_2026/7lkh_23408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lkh_23408/07_2026/7lkh_23408.map" } resolution = 3.5 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= -0.000 sd= 0.005 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 8 5.16 5 C 2661 2.51 5 N 717 2.21 5 O 793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 4179 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2338 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 22, 'TRANS': 263} Chain breaks: 2 Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "L" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 854 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.71, per 1000 atoms: 0.17 Number of scatterers: 4179 At special positions: 0 Unit cell: (70.2, 100.44, 88.56, 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 8 16.00 O 793 8.00 N 717 7.00 C 2661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 169 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 667 " Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 108.2 milliseconds 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 976 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 8 sheets defined 25.6% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 115 through 121 removed outlier: 3.667A pdb=" N ARG A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.925A pdb=" N LEU A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 181 through 187 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 208 through 215 Processing helix chain 'A' and resid 244 through 259 Processing helix chain 'A' and resid 644 through 648 Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 657 through 665 Processing helix chain 'A' and resid 688 through 695 Processing helix chain 'A' and resid 697 through 701 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.745A pdb=" N GLN H 65 " --> pdb=" O PRO H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.765A pdb=" N ILE L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 64 removed outlier: 6.711A pdb=" N VAL A 61 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N HIS A 273 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP A 63 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N HIS A 275 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 64 removed outlier: 6.711A pdb=" N VAL A 61 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N HIS A 273 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP A 63 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N HIS A 275 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ILE A 681 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN A 95 " --> pdb=" O ILE A 681 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL A 683 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE A 97 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU A 685 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS A 99 " --> pdb=" O LEU A 685 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU A 687 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR A 101 " --> pdb=" O LEU A 687 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 150 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.429A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.924A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 151 hydrogen bonds defined for protein. 348 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.68 Time building geometry restraints manager: 0.38 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: 1333 1.34 - 1.46: 1038 1.46 - 1.58: 1904 1.58 - 1.71: 0 1.71 - 1.83: 9 Bond restraints: 4284 Sorted by residual: bond pdb=" N VAL A 55 " pdb=" CA VAL A 55 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.19e-02 7.06e+03 1.23e+01 bond pdb=" N THR A 59 " pdb=" CA THR A 59 " ideal model delta sigma weight residual 1.462 1.491 -0.029 8.50e-03 1.38e+04 1.19e+01 bond pdb=" N VAL A 61 " pdb=" CA VAL A 61 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.32e-02 5.74e+03 6.85e+00 bond pdb=" N LYS A 62 " pdb=" CA LYS A 62 " ideal model delta sigma weight residual 1.453 1.485 -0.032 1.31e-02 5.83e+03 5.86e+00 bond pdb=" N GLY A 53 " pdb=" CA GLY A 53 " ideal model delta sigma weight residual 1.451 1.488 -0.037 1.60e-02 3.91e+03 5.31e+00 ... (remaining 4279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 5485 1.82 - 3.65: 282 3.65 - 5.47: 52 5.47 - 7.29: 6 7.29 - 9.12: 2 Bond angle restraints: 5827 Sorted by residual: angle pdb=" C LEU L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta sigma weight residual 119.84 113.38 6.46 1.25e+00 6.40e-01 2.67e+01 angle pdb=" C ASP A 83 " pdb=" N TRP A 84 " pdb=" CA TRP A 84 " ideal model delta sigma weight residual 121.54 130.66 -9.12 1.91e+00 2.74e-01 2.28e+01 angle pdb=" CA VAL A 61 " pdb=" C VAL A 61 " pdb=" O VAL A 61 " ideal model delta sigma weight residual 121.59 117.51 4.08 1.03e+00 9.43e-01 1.57e+01 angle pdb=" CA LYS A 62 " pdb=" C LYS A 62 " pdb=" O LYS A 62 " ideal model delta sigma weight residual 121.81 117.32 4.49 1.18e+00 7.18e-01 1.45e+01 angle pdb=" CA ARG A 673 " pdb=" C ARG A 673 " pdb=" O ARG A 673 " ideal model delta sigma weight residual 121.60 117.02 4.58 1.21e+00 6.83e-01 1.43e+01 ... (remaining 5822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 2312 16.91 - 33.81: 185 33.81 - 50.71: 33 50.71 - 67.62: 4 67.62 - 84.52: 8 Dihedral angle restraints: 2542 sinusoidal: 1028 harmonic: 1514 Sorted by residual: dihedral pdb=" CA THR L 93 " pdb=" C THR L 93 " pdb=" N LEU L 94 " pdb=" CA LEU L 94 " ideal model delta harmonic sigma weight residual -180.00 -152.11 -27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA PRO A 155 " pdb=" C PRO A 155 " pdb=" N GLY A 156 " pdb=" CA GLY A 156 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ARG H 98 " pdb=" C ARG H 98 " pdb=" N TYR H 99 " pdb=" CA TYR H 99 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 2539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 421 0.042 - 0.084: 140 0.084 - 0.126: 65 0.126 - 0.169: 19 0.169 - 0.211: 3 Chirality restraints: 648 Sorted by residual: chirality pdb=" CA LYS A 256 " pdb=" N LYS A 256 " pdb=" C LYS A 256 " pdb=" CB LYS A 256 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA PHE A 65 " pdb=" N PHE A 65 " pdb=" C PHE A 65 " pdb=" CB PHE A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ARG L 53 " pdb=" N ARG L 53 " pdb=" C ARG L 53 " pdb=" CB ARG L 53 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.14e-01 ... (remaining 645 not shown) Planarity restraints: 744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG H 40 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO H 41 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 154 " -0.065 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO A 155 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 155 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 155 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 65 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.28e+00 pdb=" N PRO A 66 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.032 5.00e-02 4.00e+02 ... (remaining 741 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 26 2.50 - 3.10: 3058 3.10 - 3.70: 5794 3.70 - 4.30: 8688 4.30 - 4.90: 14923 Nonbonded interactions: 32489 Sorted by model distance: nonbonded pdb=" O4 NAG B 1 " pdb=" O7 NAG B 2 " model vdw 1.903 3.040 nonbonded pdb=" OD2 ASP H 73 " pdb=" OG SER H 76 " model vdw 2.057 3.040 nonbonded pdb=" O GLY A 87 " pdb=" OH TYR A 674 " model vdw 2.096 3.040 nonbonded pdb=" O ASN L 77 " pdb=" OD1 ASN L 77 " model vdw 2.245 3.040 nonbonded pdb=" O PHE A 276 " pdb=" O ALA A 671 " model vdw 2.276 3.040 ... (remaining 32484 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.640 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.650 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 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 : 0.006 0.064 4289 Z= 0.294 Angle : 0.943 9.116 5839 Z= 0.565 Chirality : 0.054 0.211 648 Planarity : 0.007 0.112 743 Dihedral : 13.234 84.519 1557 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.22 % Allowed : 0.43 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.99 (0.37), residues: 506 helix: -0.11 (0.59), residues: 80 sheet: -0.14 (0.39), residues: 171 loop : -1.16 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 230 TYR 0.031 0.003 TYR A 64 PHE 0.037 0.003 PHE A 65 TRP 0.014 0.002 TRP H 47 HIS 0.004 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.29 ( 4284) covalent geometry : angle 0.93829 / 0.56 ( 5827) SS BOND : bond 0.00750 / 0.43 ( 3) SS BOND : angle 1.90820 / 0.80 ( 6) hydrogen bonds : bond 0.12001 / 7.43 ( 141) hydrogen bonds : angle 5.63991 / 3.66 ( 348) link_BETA1-4 : bond 0.01006 / 0.63 ( 1) link_BETA1-4 : angle 2.94743 / 1.17 ( 3) link_NAG-ASN : bond 0.01075 / 0.67 ( 1) link_NAG-ASN : angle 2.07839 / 1.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.115 Fit side-chains REVERT: A 138 SER cc_start: 0.8344 (t) cc_final: 0.8138 (t) REVERT: L 108 ARG cc_start: 0.4258 (ppt170) cc_final: 0.4046 (ppt170) outliers start: 1 outliers final: 1 residues processed: 80 average time/residue: 0.0635 time to fit residues: 6.2960 Evaluate side-chains 52 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN A 167 HIS ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.156929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.130033 restraints weight = 5612.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.133664 restraints weight = 3397.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136164 restraints weight = 2469.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.137786 restraints weight = 1994.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.138784 restraints weight = 1719.873| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4289 Z= 0.191 Angle : 0.733 14.164 5839 Z= 0.362 Chirality : 0.048 0.167 648 Planarity : 0.006 0.074 743 Dihedral : 5.091 38.961 571 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.17 % Allowed : 6.30 % Favored : 91.52 % 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: -0.56 (0.37), residues: 506 helix: 0.18 (0.60), residues: 72 sheet: -0.10 (0.38), residues: 165 loop : -0.63 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 267 TYR 0.038 0.002 TYR H 99 PHE 0.013 0.002 PHE A 663 TRP 0.011 0.001 TRP A 84 HIS 0.003 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 ( 4284) covalent geometry : angle 0.72822 / 0.36 ( 5827) SS BOND : bond 0.00837 / 0.51 ( 3) SS BOND : angle 0.72121 / 0.32 ( 6) hydrogen bonds : bond 0.03874 / 2.50 ( 141) hydrogen bonds : angle 5.17315 / 3.39 ( 348) link_BETA1-4 : bond 0.00841 / 0.53 ( 1) link_BETA1-4 : angle 3.53137 / 1.48 ( 3) link_NAG-ASN : bond 0.01193 / 0.75 ( 1) link_NAG-ASN : angle 1.79023 / 1.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.163 Fit side-chains REVERT: A 62 LYS cc_start: 0.7380 (mttt) cc_final: 0.6501 (mppt) REVERT: A 244 ASP cc_start: 0.7217 (t70) cc_final: 0.6809 (t70) outliers start: 10 outliers final: 5 residues processed: 72 average time/residue: 0.0702 time to fit residues: 6.5471 Evaluate side-chains 57 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 44 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN ** A 198 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 = 0.3764 r_free = 0.3764 target = 0.159597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.132191 restraints weight = 5613.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135917 restraints weight = 3435.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.138398 restraints weight = 2513.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.140084 restraints weight = 2039.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.140875 restraints weight = 1761.802| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4289 Z= 0.147 Angle : 0.659 13.118 5839 Z= 0.324 Chirality : 0.046 0.162 648 Planarity : 0.005 0.054 743 Dihedral : 4.470 19.278 569 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.96 % Allowed : 9.35 % Favored : 88.70 % 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: -0.28 (0.38), residues: 506 helix: 0.40 (0.61), residues: 72 sheet: 0.04 (0.39), residues: 167 loop : -0.41 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 267 TYR 0.032 0.002 TYR H 99 PHE 0.009 0.001 PHE L 98 TRP 0.012 0.001 TRP A 84 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 4284) covalent geometry : angle 0.65566 / 0.32 ( 5827) SS BOND : bond 0.00772 / 0.47 ( 3) SS BOND : angle 0.90504 / 0.42 ( 6) hydrogen bonds : bond 0.03367 / 2.22 ( 141) hydrogen bonds : angle 4.90079 / 3.24 ( 348) link_BETA1-4 : bond 0.00942 / 0.59 ( 1) link_BETA1-4 : angle 2.88436 / 1.23 ( 3) link_NAG-ASN : bond 0.00649 / 0.41 ( 1) link_NAG-ASN : angle 1.25593 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.103 Fit side-chains REVERT: A 62 LYS cc_start: 0.7431 (mttt) cc_final: 0.6541 (mppt) REVERT: H 87 THR cc_start: 0.7864 (m) cc_final: 0.7396 (p) REVERT: L 28 ASP cc_start: 0.8021 (p0) cc_final: 0.7729 (p0) outliers start: 9 outliers final: 7 residues processed: 74 average time/residue: 0.0646 time to fit residues: 6.1539 Evaluate side-chains 62 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN ** A 198 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 = 0.3618 r_free = 0.3618 target = 0.145728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118351 restraints weight = 5669.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.121593 restraints weight = 3599.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123771 restraints weight = 2690.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.125165 restraints weight = 2209.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.126217 restraints weight = 1942.807| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4289 Z= 0.147 Angle : 0.650 11.960 5839 Z= 0.318 Chirality : 0.045 0.157 648 Planarity : 0.005 0.047 743 Dihedral : 4.357 18.108 569 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.26 % Allowed : 9.78 % Favored : 86.96 % 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: -0.16 (0.39), residues: 506 helix: 0.53 (0.60), residues: 72 sheet: 0.07 (0.39), residues: 167 loop : -0.31 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.029 0.002 TYR H 99 PHE 0.008 0.001 PHE A 663 TRP 0.012 0.001 TRP A 84 HIS 0.002 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 4284) covalent geometry : angle 0.64681 / 0.32 ( 5827) SS BOND : bond 0.00328 / 0.17 ( 3) SS BOND : angle 0.69387 / 0.32 ( 6) hydrogen bonds : bond 0.03288 / 2.20 ( 141) hydrogen bonds : angle 4.83391 / 3.20 ( 348) link_BETA1-4 : bond 0.00889 / 0.56 ( 1) link_BETA1-4 : angle 2.64615 / 1.13 ( 3) link_NAG-ASN : bond 0.00710 / 0.44 ( 1) link_NAG-ASN : angle 1.41516 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.159 Fit side-chains REVERT: A 62 LYS cc_start: 0.7361 (mttt) cc_final: 0.6022 (mptt) REVERT: H 87 THR cc_start: 0.7882 (m) cc_final: 0.7367 (p) REVERT: L 28 ASP cc_start: 0.8063 (p0) cc_final: 0.7804 (p0) REVERT: L 34 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8439 (m-40) outliers start: 15 outliers final: 10 residues processed: 71 average time/residue: 0.0658 time to fit residues: 6.1124 Evaluate side-chains 65 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 0.1980 chunk 17 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 11 optimal weight: 0.0020 chunk 25 optimal weight: 0.9990 overall best weight: 0.3746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.159293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.132361 restraints weight = 5530.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136083 restraints weight = 3358.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.138602 restraints weight = 2428.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.140228 restraints weight = 1952.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.141200 restraints weight = 1690.374| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 4289 Z= 0.109 Angle : 0.603 11.975 5839 Z= 0.294 Chirality : 0.043 0.145 648 Planarity : 0.004 0.042 743 Dihedral : 4.146 17.359 569 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.61 % Allowed : 11.74 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.18 (0.38), residues: 506 helix: 0.56 (0.60), residues: 75 sheet: 0.10 (0.39), residues: 165 loop : -0.38 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.025 0.001 TYR H 99 PHE 0.007 0.001 PHE L 98 TRP 0.013 0.001 TRP A 84 HIS 0.010 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 4284) covalent geometry : angle 0.60048 / 0.29 ( 5827) SS BOND : bond 0.00277 / 0.14 ( 3) SS BOND : angle 0.61344 / 0.28 ( 6) hydrogen bonds : bond 0.02937 / 1.98 ( 141) hydrogen bonds : angle 4.63892 / 3.07 ( 348) link_BETA1-4 : bond 0.00926 / 0.58 ( 1) link_BETA1-4 : angle 2.31197 / 0.95 ( 3) link_NAG-ASN : bond 0.00364 / 0.23 ( 1) link_NAG-ASN : angle 1.16460 / 0.65 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.125 Fit side-chains REVERT: A 62 LYS cc_start: 0.7248 (mttt) cc_final: 0.6348 (mppt) REVERT: H 87 THR cc_start: 0.7841 (m) cc_final: 0.7333 (p) REVERT: L 28 ASP cc_start: 0.8040 (p0) cc_final: 0.7806 (p0) outliers start: 12 outliers final: 11 residues processed: 72 average time/residue: 0.0608 time to fit residues: 5.6368 Evaluate side-chains 67 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN A 180 ASN H 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.158052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.130864 restraints weight = 5670.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.134524 restraints weight = 3429.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.136954 restraints weight = 2495.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.138487 restraints weight = 2021.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.139571 restraints weight = 1752.832| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4289 Z= 0.153 Angle : 0.628 11.565 5839 Z= 0.312 Chirality : 0.044 0.149 648 Planarity : 0.005 0.062 743 Dihedral : 4.214 16.884 569 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.26 % Allowed : 12.17 % Favored : 84.57 % 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: -0.17 (0.38), residues: 506 helix: 0.47 (0.60), residues: 73 sheet: 0.16 (0.39), residues: 163 loop : -0.36 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 267 TYR 0.027 0.002 TYR H 99 PHE 0.008 0.001 PHE A 247 TRP 0.010 0.001 TRP A 84 HIS 0.011 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 4284) covalent geometry : angle 0.62592 / 0.31 ( 5827) SS BOND : bond 0.00307 / 0.15 ( 3) SS BOND : angle 0.53269 / 0.23 ( 6) hydrogen bonds : bond 0.03334 / 2.26 ( 141) hydrogen bonds : angle 4.70856 / 3.11 ( 348) link_BETA1-4 : bond 0.00790 / 0.49 ( 1) link_BETA1-4 : angle 1.77416 / 0.76 ( 3) link_NAG-ASN : bond 0.00792 / 0.50 ( 1) link_NAG-ASN : angle 1.88383 / 1.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.093 Fit side-chains REVERT: H 91 THR cc_start: 0.8799 (p) cc_final: 0.8584 (p) REVERT: L 28 ASP cc_start: 0.8010 (p0) cc_final: 0.7804 (p0) outliers start: 15 outliers final: 12 residues processed: 72 average time/residue: 0.0576 time to fit residues: 5.3460 Evaluate side-chains 72 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 26 optimal weight: 0.0570 chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 0.0770 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.158285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.131185 restraints weight = 5650.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.134946 restraints weight = 3404.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137423 restraints weight = 2454.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138891 restraints weight = 1978.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.140030 restraints weight = 1717.573| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4289 Z= 0.113 Angle : 0.599 11.589 5839 Z= 0.292 Chirality : 0.043 0.141 648 Planarity : 0.005 0.049 743 Dihedral : 4.073 16.768 569 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.83 % Allowed : 13.26 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.10 (0.38), residues: 506 helix: 0.65 (0.61), residues: 73 sheet: 0.17 (0.39), residues: 164 loop : -0.34 (0.41), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 267 TYR 0.024 0.001 TYR H 99 PHE 0.007 0.001 PHE A 663 TRP 0.013 0.001 TRP A 84 HIS 0.008 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 4284) covalent geometry : angle 0.59710 / 0.29 ( 5827) SS BOND : bond 0.00287 / 0.15 ( 3) SS BOND : angle 0.53981 / 0.24 ( 6) hydrogen bonds : bond 0.03048 / 2.08 ( 141) hydrogen bonds : angle 4.61719 / 3.06 ( 348) link_BETA1-4 : bond 0.00880 / 0.55 ( 1) link_BETA1-4 : angle 1.70696 / 0.75 ( 3) link_NAG-ASN : bond 0.00418 / 0.26 ( 1) link_NAG-ASN : angle 1.34418 / 0.81 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.153 Fit side-chains REVERT: H 91 THR cc_start: 0.8767 (p) cc_final: 0.8558 (p) outliers start: 13 outliers final: 11 residues processed: 73 average time/residue: 0.0548 time to fit residues: 5.2270 Evaluate side-chains 71 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.0870 chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 0.0170 chunk 1 optimal weight: 0.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.158021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.130723 restraints weight = 5577.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.134372 restraints weight = 3406.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.136793 restraints weight = 2491.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.138449 restraints weight = 2020.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.139409 restraints weight = 1748.585| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4289 Z= 0.128 Angle : 0.604 11.380 5839 Z= 0.301 Chirality : 0.043 0.140 648 Planarity : 0.005 0.043 743 Dihedral : 4.053 16.827 569 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.83 % Allowed : 13.26 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.10 (0.38), residues: 506 helix: 0.56 (0.60), residues: 73 sheet: 0.22 (0.39), residues: 162 loop : -0.34 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 267 TYR 0.024 0.002 TYR H 99 PHE 0.012 0.001 PHE L 87 TRP 0.011 0.001 TRP A 84 HIS 0.008 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 4284) covalent geometry : angle 0.60216 / 0.30 ( 5827) SS BOND : bond 0.00332 / 0.17 ( 3) SS BOND : angle 0.55026 / 0.26 ( 6) hydrogen bonds : bond 0.03132 / 2.14 ( 141) hydrogen bonds : angle 4.56051 / 3.01 ( 348) link_BETA1-4 : bond 0.00692 / 0.43 ( 1) link_BETA1-4 : angle 1.52378 / 0.69 ( 3) link_NAG-ASN : bond 0.00552 / 0.34 ( 1) link_NAG-ASN : angle 1.47256 / 0.89 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.159 Fit side-chains REVERT: H 91 THR cc_start: 0.8774 (p) cc_final: 0.8545 (p) outliers start: 13 outliers final: 13 residues processed: 73 average time/residue: 0.0570 time to fit residues: 5.5470 Evaluate side-chains 75 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 0.0030 chunk 24 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.159678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.132479 restraints weight = 5658.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136152 restraints weight = 3438.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.138644 restraints weight = 2492.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.140145 restraints weight = 2010.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.141304 restraints weight = 1746.614| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4289 Z= 0.109 Angle : 0.595 11.521 5839 Z= 0.291 Chirality : 0.042 0.134 648 Planarity : 0.004 0.041 743 Dihedral : 3.938 16.455 569 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.61 % Allowed : 13.91 % Favored : 83.48 % 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: 0.01 (0.39), residues: 506 helix: 0.67 (0.61), residues: 73 sheet: 0.42 (0.40), residues: 157 loop : -0.37 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 267 TYR 0.022 0.001 TYR H 99 PHE 0.006 0.001 PHE L 98 TRP 0.015 0.001 TRP A 84 HIS 0.008 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 4284) covalent geometry : angle 0.59320 / 0.29 ( 5827) SS BOND : bond 0.00315 / 0.16 ( 3) SS BOND : angle 0.55969 / 0.26 ( 6) hydrogen bonds : bond 0.02922 / 2.01 ( 141) hydrogen bonds : angle 4.48239 / 2.98 ( 348) link_BETA1-4 : bond 0.00747 / 0.47 ( 1) link_BETA1-4 : angle 1.55031 / 0.72 ( 3) link_NAG-ASN : bond 0.00336 / 0.21 ( 1) link_NAG-ASN : angle 1.18835 / 0.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.157 Fit side-chains REVERT: H 91 THR cc_start: 0.8752 (p) cc_final: 0.8521 (p) REVERT: H 99 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.5903 (p90) outliers start: 12 outliers final: 10 residues processed: 73 average time/residue: 0.0518 time to fit residues: 5.0322 Evaluate side-chains 70 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 0.0050 chunk 28 optimal weight: 3.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.159425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.132401 restraints weight = 5528.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.136030 restraints weight = 3371.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.138459 restraints weight = 2461.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.140058 restraints weight = 1992.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140878 restraints weight = 1725.415| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4289 Z= 0.118 Angle : 0.604 11.439 5839 Z= 0.296 Chirality : 0.043 0.136 648 Planarity : 0.004 0.041 743 Dihedral : 3.929 16.515 569 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.39 % Allowed : 13.91 % Favored : 83.70 % 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: -0.01 (0.39), residues: 506 helix: 0.57 (0.61), residues: 73 sheet: 0.43 (0.40), residues: 157 loop : -0.36 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 267 TYR 0.023 0.001 TYR H 99 PHE 0.013 0.001 PHE L 87 TRP 0.012 0.001 TRP A 84 HIS 0.009 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 4284) covalent geometry : angle 0.60246 / 0.30 ( 5827) SS BOND : bond 0.00319 / 0.16 ( 3) SS BOND : angle 0.56476 / 0.26 ( 6) hydrogen bonds : bond 0.02966 / 2.04 ( 141) hydrogen bonds : angle 4.47746 / 2.98 ( 348) link_BETA1-4 : bond 0.00743 / 0.46 ( 1) link_BETA1-4 : angle 1.47635 / 0.69 ( 3) link_NAG-ASN : bond 0.00440 / 0.27 ( 1) link_NAG-ASN : angle 1.32762 / 0.79 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.134 Fit side-chains REVERT: A 184 ARG cc_start: 0.7558 (ttm110) cc_final: 0.7256 (ttp-170) REVERT: H 91 THR cc_start: 0.8778 (p) cc_final: 0.8559 (p) REVERT: H 99 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.6053 (p90) outliers start: 11 outliers final: 9 residues processed: 68 average time/residue: 0.0595 time to fit residues: 5.3496 Evaluate side-chains 70 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.0270 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.161328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134401 restraints weight = 5577.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.137960 restraints weight = 3398.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.140368 restraints weight = 2474.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.141847 restraints weight = 2005.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.143007 restraints weight = 1744.514| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4289 Z= 0.120 Angle : 0.600 11.426 5839 Z= 0.295 Chirality : 0.043 0.138 648 Planarity : 0.004 0.041 743 Dihedral : 3.940 16.335 569 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.83 % Allowed : 14.35 % Favored : 82.83 % 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: -0.05 (0.38), residues: 506 helix: 0.44 (0.60), residues: 75 sheet: 0.42 (0.40), residues: 157 loop : -0.38 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 267 TYR 0.023 0.001 TYR H 99 PHE 0.007 0.001 PHE A 663 TRP 0.012 0.001 TRP A 84 HIS 0.009 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 4284) covalent geometry : angle 0.59873 / 0.29 ( 5827) SS BOND : bond 0.00328 / 0.17 ( 3) SS BOND : angle 0.61412 / 0.28 ( 6) hydrogen bonds : bond 0.02988 / 2.05 ( 141) hydrogen bonds : angle 4.43948 / 2.95 ( 348) link_BETA1-4 : bond 0.00699 / 0.44 ( 1) link_BETA1-4 : angle 1.42111 / 0.67 ( 3) link_NAG-ASN : bond 0.00476 / 0.30 ( 1) link_NAG-ASN : angle 1.38536 / 0.83 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 895.58 seconds wall clock time: 16 minutes 2.11 seconds (962.11 seconds total)