Starting phenix.real_space_refine on Thu Mar 6 00:46:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lkh_23408/03_2025/7lkh_23408.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lkh_23408/03_2025/7lkh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7lkh_23408/03_2025/7lkh_23408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lkh_23408/03_2025/7lkh_23408.map" model { file = "/net/cci-nas-00/data/ceres_data/7lkh_23408/03_2025/7lkh_23408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lkh_23408/03_2025/7lkh_23408.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.92, per 1000 atoms: 0.70 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: 0.91 Conformation dependent library (CDL) restraints added in 612.8 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: 0.52 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: 1.11 Time building geometry restraints manager: 1.12 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: 2350 16.91 - 33.81: 185 33.81 - 50.71: 35 50.71 - 67.62: 6 67.62 - 84.52: 8 Dihedral angle restraints: 2584 sinusoidal: 1070 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 2581 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: 0.810 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.180 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 4284 Z= 0.388 Angle : 0.938 9.116 5827 Z= 0.565 Chirality : 0.054 0.211 648 Planarity : 0.007 0.112 743 Dihedral : 13.326 84.519 1599 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.002 TRP H 47 HIS 0.004 0.001 HIS A 273 PHE 0.037 0.003 PHE A 65 TYR 0.031 0.003 TYR A 64 ARG 0.013 0.001 ARG A 230 *********************** 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 : 0.424 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: 0.1931 time to fit residues: 18.9170 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 : 0.445 ------------------------------------------------------------------------------- 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 42 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3753 r_free = 0.3753 target = 0.158303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131502 restraints weight = 5550.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135274 restraints weight = 3369.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.137712 restraints weight = 2437.861| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4284 Z= 0.251 Angle : 0.712 14.069 5827 Z= 0.351 Chirality : 0.048 0.164 648 Planarity : 0.006 0.070 743 Dihedral : 6.282 59.155 613 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.17 % Allowed : 6.09 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.37), residues: 506 helix: 0.25 (0.60), residues: 72 sheet: -0.06 (0.38), residues: 165 loop : -0.60 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 84 HIS 0.003 0.001 HIS A 167 PHE 0.011 0.002 PHE L 98 TYR 0.036 0.002 TYR H 99 ARG 0.005 0.001 ARG A 267 *********************** 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 71 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.576 Fit side-chains REVERT: A 62 LYS cc_start: 0.7335 (mttt) cc_final: 0.6534 (mppt) REVERT: A 244 ASP cc_start: 0.7169 (t70) cc_final: 0.6790 (t70) outliers start: 10 outliers final: 5 residues processed: 69 average time/residue: 0.1499 time to fit residues: 13.8915 Evaluate side-chains 54 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 0.0050 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.159332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132315 restraints weight = 5573.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.136069 restraints weight = 3385.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.138533 restraints weight = 2456.501| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4284 Z= 0.189 Angle : 0.643 13.304 5827 Z= 0.314 Chirality : 0.045 0.158 648 Planarity : 0.005 0.051 743 Dihedral : 5.498 53.374 611 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.74 % Allowed : 8.91 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.38), residues: 506 helix: 0.54 (0.61), residues: 72 sheet: 0.09 (0.39), residues: 167 loop : -0.42 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 84 HIS 0.002 0.001 HIS A 198 PHE 0.008 0.001 PHE L 98 TYR 0.030 0.002 TYR H 99 ARG 0.003 0.000 ARG A 652 *********************** 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 78 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.466 Fit side-chains REVERT: A 62 LYS cc_start: 0.7404 (mttt) cc_final: 0.6669 (mppt) REVERT: H 87 THR cc_start: 0.7842 (m) cc_final: 0.7389 (p) outliers start: 8 outliers final: 6 residues processed: 77 average time/residue: 0.1603 time to fit residues: 15.7067 Evaluate side-chains 61 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 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 17 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 1 optimal weight: 0.0470 chunk 46 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN H 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.159217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.132293 restraints weight = 5550.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.136030 restraints weight = 3354.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.138542 restraints weight = 2419.464| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4284 Z= 0.174 Angle : 0.626 12.237 5827 Z= 0.304 Chirality : 0.044 0.150 648 Planarity : 0.005 0.059 743 Dihedral : 5.052 46.575 611 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.26 % Allowed : 10.00 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.39), residues: 506 helix: 0.77 (0.62), residues: 72 sheet: 0.10 (0.39), residues: 166 loop : -0.27 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 84 HIS 0.001 0.001 HIS A 196 PHE 0.007 0.001 PHE L 98 TYR 0.026 0.002 TYR H 99 ARG 0.003 0.000 ARG A 267 *********************** 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 72 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.465 Fit side-chains REVERT: A 62 LYS cc_start: 0.7380 (mttt) cc_final: 0.6448 (mppt) REVERT: H 87 THR cc_start: 0.7887 (m) cc_final: 0.7325 (p) REVERT: L 28 ASP cc_start: 0.7889 (p0) cc_final: 0.7611 (p0) REVERT: L 34 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8549 (m-40) outliers start: 15 outliers final: 11 residues processed: 68 average time/residue: 0.1378 time to fit residues: 12.3970 Evaluate side-chains 64 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 A residue 272 VAL 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 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 41 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 0.0470 chunk 7 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN A 180 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.157942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.130814 restraints weight = 5635.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.134645 restraints weight = 3392.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.137161 restraints weight = 2440.645| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4284 Z= 0.197 Angle : 0.627 12.124 5827 Z= 0.305 Chirality : 0.045 0.154 648 Planarity : 0.005 0.046 743 Dihedral : 4.839 40.867 611 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.26 % Allowed : 11.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.39), residues: 506 helix: 0.70 (0.61), residues: 73 sheet: 0.11 (0.39), residues: 165 loop : -0.28 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 84 HIS 0.002 0.001 HIS A 196 PHE 0.009 0.001 PHE A 663 TYR 0.026 0.002 TYR H 99 ARG 0.003 0.000 ARG A 267 *********************** 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 79 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.461 Fit side-chains REVERT: A 62 LYS cc_start: 0.7347 (mttt) cc_final: 0.6292 (mppt) REVERT: L 28 ASP cc_start: 0.8088 (p0) cc_final: 0.7849 (p0) REVERT: L 34 ASN cc_start: 0.8741 (OUTLIER) cc_final: 0.8501 (m-40) outliers start: 15 outliers final: 13 residues processed: 74 average time/residue: 0.1503 time to fit residues: 14.4266 Evaluate side-chains 71 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 A residue 264 CYS Chi-restraints excluded: chain A residue 272 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 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 26 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 0.0010 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.160634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133548 restraints weight = 5533.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.137269 restraints weight = 3366.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.139734 restraints weight = 2452.596| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4284 Z= 0.176 Angle : 0.609 11.814 5827 Z= 0.296 Chirality : 0.044 0.159 648 Planarity : 0.004 0.043 743 Dihedral : 4.639 35.390 611 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.48 % Allowed : 11.74 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.39), residues: 506 helix: 0.76 (0.61), residues: 73 sheet: 0.15 (0.39), residues: 165 loop : -0.25 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 84 HIS 0.002 0.001 HIS A 196 PHE 0.008 0.001 PHE A 663 TYR 0.025 0.001 TYR H 99 ARG 0.006 0.000 ARG A 267 *********************** 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 74 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.451 Fit side-chains REVERT: A 62 LYS cc_start: 0.7315 (mttt) cc_final: 0.6206 (mppt) REVERT: L 28 ASP cc_start: 0.8096 (p0) cc_final: 0.7879 (p0) outliers start: 16 outliers final: 12 residues processed: 68 average time/residue: 0.1706 time to fit residues: 15.0759 Evaluate side-chains 71 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 163 LEU 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 272 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.157138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.129898 restraints weight = 5512.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133609 restraints weight = 3360.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.136025 restraints weight = 2442.985| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4284 Z= 0.215 Angle : 0.623 11.661 5827 Z= 0.306 Chirality : 0.045 0.169 648 Planarity : 0.005 0.044 743 Dihedral : 4.597 29.715 611 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.48 % Allowed : 12.39 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.39), residues: 506 helix: 0.68 (0.61), residues: 73 sheet: 0.16 (0.39), residues: 163 loop : -0.31 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 84 HIS 0.002 0.001 HIS A 196 PHE 0.009 0.001 PHE A 663 TYR 0.026 0.002 TYR H 99 ARG 0.006 0.000 ARG A 267 *********************** 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 81 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.500 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 74 average time/residue: 0.1453 time to fit residues: 14.1308 Evaluate side-chains 74 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 272 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.0270 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 2 optimal weight: 0.0070 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.161060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.134024 restraints weight = 5518.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.137705 restraints weight = 3377.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.140142 restraints weight = 2465.839| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4284 Z= 0.165 Angle : 0.613 11.562 5827 Z= 0.299 Chirality : 0.043 0.161 648 Planarity : 0.004 0.041 743 Dihedral : 4.336 23.165 611 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.83 % Allowed : 13.04 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.39), residues: 506 helix: 0.70 (0.61), residues: 75 sheet: 0.19 (0.39), residues: 164 loop : -0.30 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 84 HIS 0.001 0.000 HIS A 198 PHE 0.011 0.001 PHE L 87 TYR 0.024 0.001 TYR H 99 ARG 0.007 0.000 ARG A 267 *********************** 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 74 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.503 Fit side-chains REVERT: H 87 THR cc_start: 0.7823 (m) cc_final: 0.7240 (p) outliers start: 13 outliers final: 11 residues processed: 69 average time/residue: 0.1493 time to fit residues: 13.6440 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 : 0.534 ------------------------------------------------------------------------------- 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 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 93 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 9 optimal weight: 0.0370 chunk 14 optimal weight: 3.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.159233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132025 restraints weight = 5521.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.135707 restraints weight = 3374.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.138172 restraints weight = 2461.570| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4284 Z= 0.163 Angle : 0.592 11.515 5827 Z= 0.292 Chirality : 0.043 0.158 648 Planarity : 0.004 0.041 743 Dihedral : 4.232 17.844 611 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.83 % Allowed : 12.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.39), residues: 506 helix: 0.83 (0.62), residues: 73 sheet: 0.41 (0.40), residues: 157 loop : -0.34 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 84 HIS 0.002 0.000 HIS A 198 PHE 0.007 0.001 PHE A 65 TYR 0.023 0.001 TYR H 99 ARG 0.007 0.000 ARG A 267 *********************** 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 78 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.463 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 74 average time/residue: 0.1342 time to fit residues: 13.0691 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 : 0.430 ------------------------------------------------------------------------------- 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 74 THR 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 47 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.0010 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.158789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.131530 restraints weight = 5524.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135186 restraints weight = 3405.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.137638 restraints weight = 2483.664| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4284 Z= 0.188 Angle : 0.617 11.385 5827 Z= 0.301 Chirality : 0.044 0.152 648 Planarity : 0.004 0.041 743 Dihedral : 4.282 18.495 611 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.61 % Allowed : 13.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.39), residues: 506 helix: 0.65 (0.60), residues: 75 sheet: 0.40 (0.40), residues: 157 loop : -0.36 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 84 HIS 0.002 0.001 HIS A 198 PHE 0.013 0.001 PHE L 87 TYR 0.024 0.002 TYR H 99 ARG 0.007 0.000 ARG A 267 ********************** 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 72 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.434 Fit side-chains REVERT: A 184 ARG cc_start: 0.7632 (ttm110) cc_final: 0.7361 (ttp-170) outliers start: 12 outliers final: 11 residues processed: 70 average time/residue: 0.1436 time to fit residues: 13.2510 Evaluate side-chains 69 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 33 optimal weight: 0.1980 chunk 1 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.154130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.126139 restraints weight = 5575.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.129766 restraints weight = 3486.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.132153 restraints weight = 2569.308| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4284 Z= 0.170 Angle : 0.596 11.459 5827 Z= 0.294 Chirality : 0.043 0.154 648 Planarity : 0.004 0.041 743 Dihedral : 4.269 20.240 611 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.39), residues: 506 helix: 0.71 (0.61), residues: 75 sheet: 0.41 (0.40), residues: 157 loop : -0.34 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 84 HIS 0.002 0.000 HIS A 198 PHE 0.007 0.001 PHE A 65 TYR 0.023 0.001 TYR H 99 ARG 0.007 0.000 ARG A 267 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1936.51 seconds wall clock time: 34 minutes 36.69 seconds (2076.69 seconds total)