Starting phenix.real_space_refine on Tue Feb 11 05:24:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lkh_23408/02_2025/7lkh_23408.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lkh_23408/02_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_23408/02_2025/7lkh_23408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lkh_23408/02_2025/7lkh_23408.map" model { file = "/net/cci-nas-00/data/ceres_data/7lkh_23408/02_2025/7lkh_23408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lkh_23408/02_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-5592/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: 2.99, per 1000 atoms: 0.72 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: 1.00 Conformation dependent library (CDL) restraints added in 445.6 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: 1.16 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: 0.990 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.490 Find NCS groups from input model: 0.040 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.290 ------------------------------------------------------------------------------- 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 : 0.480 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: 0.1956 time to fit residues: 19.1443 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 : 0.448 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131503 restraints weight = 5550.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135222 restraints weight = 3368.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.137680 restraints weight = 2448.258| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 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 : 0.446 Fit side-chains REVERT: A 62 LYS cc_start: 0.7337 (mttt) cc_final: 0.6534 (mppt) REVERT: A 244 ASP cc_start: 0.7170 (t70) cc_final: 0.6788 (t70) outliers start: 10 outliers final: 5 residues processed: 69 average time/residue: 0.1449 time to fit residues: 13.0986 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 : 0.451 ------------------------------------------------------------------------------- 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: 0.7980 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.157798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.130739 restraints weight = 5584.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.134443 restraints weight = 3402.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.136925 restraints weight = 2474.377| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1963 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= 0.216 Angle : 0.658 13.195 5827 Z= 0.323 Chirality : 0.046 0.161 648 Planarity : 0.005 0.051 743 Dihedral : 5.549 53.139 611 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.96 % Allowed : 9.13 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.38), residues: 506 helix: 0.46 (0.61), residues: 72 sheet: 0.06 (0.39), residues: 167 loop : -0.42 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 84 HIS 0.003 0.001 HIS A 198 PHE 0.008 0.001 PHE L 98 TYR 0.030 0.002 TYR H 99 ARG 0.004 0.000 ARG A 267 *********************** 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 80 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.479 Fit side-chains REVERT: A 62 LYS cc_start: 0.7380 (mttt) cc_final: 0.6542 (mppt) REVERT: A 244 ASP cc_start: 0.7168 (t70) cc_final: 0.6782 (t70) REVERT: H 87 THR cc_start: 0.7844 (m) cc_final: 0.7370 (p) REVERT: L 28 ASP cc_start: 0.8041 (p0) cc_final: 0.7737 (p0) outliers start: 9 outliers final: 7 residues processed: 78 average time/residue: 0.1750 time to fit residues: 17.1498 Evaluate side-chains 63 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain L residue 75 ILE 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: 0.8980 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.140188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.112889 restraints weight = 5774.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.115965 restraints weight = 3677.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.118077 restraints weight = 2725.849| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4284 Z= 0.265 Angle : 0.683 11.603 5827 Z= 0.336 Chirality : 0.046 0.160 648 Planarity : 0.005 0.058 743 Dihedral : 5.351 46.172 611 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.48 % Allowed : 9.35 % Favored : 87.17 % 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: -0.19 (0.38), residues: 506 helix: 0.49 (0.60), residues: 72 sheet: 0.07 (0.39), residues: 164 loop : -0.34 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 84 HIS 0.003 0.001 HIS A 198 PHE 0.010 0.002 PHE A 663 TYR 0.029 0.002 TYR H 99 ARG 0.003 0.001 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 74 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.496 Fit side-chains REVERT: A 244 ASP cc_start: 0.7333 (t70) cc_final: 0.6962 (t70) REVERT: H 87 THR cc_start: 0.7888 (m) cc_final: 0.7685 (m) REVERT: L 28 ASP cc_start: 0.8131 (p0) cc_final: 0.7881 (p0) REVERT: L 34 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8428 (m-40) outliers start: 16 outliers final: 13 residues processed: 71 average time/residue: 0.1540 time to fit residues: 14.2712 Evaluate side-chains 64 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 157 LEU 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 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 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: 6.9990 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 16 optimal weight: 0.0870 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.157117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.130084 restraints weight = 5642.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133789 restraints weight = 3394.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.136281 restraints weight = 2451.741| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4284 Z= 0.230 Angle : 0.653 11.659 5827 Z= 0.320 Chirality : 0.045 0.160 648 Planarity : 0.005 0.050 743 Dihedral : 5.095 41.691 611 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.26 % Allowed : 12.39 % Favored : 84.35 % 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 (0.39), residues: 506 helix: 0.47 (0.59), residues: 74 sheet: -0.04 (0.39), residues: 165 loop : -0.29 (0.42), 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 A 663 TYR 0.028 0.002 TYR H 99 ARG 0.006 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 71 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.484 Fit side-chains REVERT: A 244 ASP cc_start: 0.7252 (t70) cc_final: 0.6911 (t70) REVERT: L 28 ASP cc_start: 0.8018 (p0) cc_final: 0.7791 (p0) outliers start: 15 outliers final: 13 residues processed: 65 average time/residue: 0.1555 time to fit residues: 13.0399 Evaluate side-chains 67 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 157 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.0270 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 H 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.158588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.131500 restraints weight = 5536.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.135159 restraints weight = 3387.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.137579 restraints weight = 2477.760| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2691 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= 0.192 Angle : 0.619 11.382 5827 Z= 0.303 Chirality : 0.044 0.167 648 Planarity : 0.005 0.047 743 Dihedral : 4.683 32.641 611 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.48 % Allowed : 13.26 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.20 (0.39), residues: 506 helix: 0.58 (0.60), residues: 75 sheet: 0.06 (0.39), residues: 164 loop : -0.37 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 84 HIS 0.002 0.001 HIS A 198 PHE 0.007 0.001 PHE L 98 TYR 0.026 0.002 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 78 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.516 Fit side-chains REVERT: A 244 ASP cc_start: 0.7307 (t70) cc_final: 0.6946 (t70) REVERT: H 91 THR cc_start: 0.8746 (p) cc_final: 0.8440 (p) outliers start: 16 outliers final: 13 residues processed: 72 average time/residue: 0.1594 time to fit residues: 14.8593 Evaluate side-chains 71 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.158336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.131161 restraints weight = 5535.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.134837 restraints weight = 3396.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.137239 restraints weight = 2474.956| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2767 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= 0.205 Angle : 0.621 11.243 5827 Z= 0.306 Chirality : 0.044 0.168 648 Planarity : 0.005 0.047 743 Dihedral : 4.605 29.093 611 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.26 % Allowed : 12.39 % Favored : 84.35 % 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: -0.21 (0.38), residues: 506 helix: 0.68 (0.61), residues: 73 sheet: 0.02 (0.39), residues: 164 loop : -0.38 (0.41), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 84 HIS 0.002 0.001 HIS A 198 PHE 0.007 0.001 PHE A 663 TYR 0.026 0.002 TYR H 99 ARG 0.007 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 78 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.453 Fit side-chains REVERT: A 244 ASP cc_start: 0.7336 (t70) cc_final: 0.6973 (t70) REVERT: H 91 THR cc_start: 0.8722 (p) cc_final: 0.8432 (p) outliers start: 15 outliers final: 14 residues processed: 73 average time/residue: 0.1449 time to fit residues: 13.7486 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 : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 146 VAL 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 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 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: 2.9990 chunk 47 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.0770 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 48 optimal weight: 5.9990 chunk 2 optimal weight: 0.0870 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.159312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.132182 restraints weight = 5523.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.135904 restraints weight = 3368.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.138344 restraints weight = 2442.795| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4284 Z= 0.152 Angle : 0.588 11.406 5827 Z= 0.289 Chirality : 0.043 0.155 648 Planarity : 0.004 0.044 743 Dihedral : 4.236 19.494 611 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.61 % Allowed : 13.04 % Favored : 84.35 % 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: -0.07 (0.39), residues: 506 helix: 0.89 (0.63), residues: 73 sheet: 0.11 (0.39), residues: 164 loop : -0.33 (0.42), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 84 HIS 0.001 0.000 HIS A 198 PHE 0.010 0.001 PHE L 87 TYR 0.022 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 81 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.487 Fit side-chains REVERT: A 244 ASP cc_start: 0.7244 (t70) cc_final: 0.6899 (t70) REVERT: H 87 THR cc_start: 0.7869 (m) cc_final: 0.7321 (p) REVERT: H 91 THR cc_start: 0.8700 (p) cc_final: 0.8412 (p) outliers start: 12 outliers final: 12 residues processed: 77 average time/residue: 0.1562 time to fit residues: 15.5312 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 : 0.505 ------------------------------------------------------------------------------- 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 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 19 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 14 optimal weight: 0.0060 overall best weight: 0.8200 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.158119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.130981 restraints weight = 5559.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.134554 restraints weight = 3416.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.137015 restraints weight = 2491.562| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4284 Z= 0.221 Angle : 0.636 11.146 5827 Z= 0.312 Chirality : 0.044 0.167 648 Planarity : 0.004 0.047 743 Dihedral : 4.447 21.139 611 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.26 % Allowed : 13.26 % 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: -0.16 (0.38), residues: 506 helix: 0.67 (0.61), residues: 73 sheet: 0.09 (0.39), residues: 162 loop : -0.37 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 84 HIS 0.002 0.001 HIS A 132 PHE 0.007 0.001 PHE A 247 TYR 0.024 0.002 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 79 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.433 Fit side-chains REVERT: A 184 ARG cc_start: 0.7594 (ttm110) cc_final: 0.7367 (ttm170) REVERT: A 244 ASP cc_start: 0.7336 (t70) cc_final: 0.7002 (t70) REVERT: H 91 THR cc_start: 0.8690 (p) cc_final: 0.8380 (p) outliers start: 15 outliers final: 13 residues processed: 74 average time/residue: 0.1455 time to fit residues: 13.9749 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 : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 146 VAL 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 21 ILE 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 47 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 0.0040 chunk 11 optimal weight: 0.2980 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.160408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133457 restraints weight = 5534.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.137044 restraints weight = 3394.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.139507 restraints weight = 2476.655| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2997 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= 0.156 Angle : 0.596 11.392 5827 Z= 0.294 Chirality : 0.043 0.155 648 Planarity : 0.004 0.045 743 Dihedral : 4.314 18.499 611 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % 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: -0.05 (0.39), residues: 506 helix: 0.80 (0.62), residues: 73 sheet: 0.27 (0.40), residues: 157 loop : -0.38 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 84 HIS 0.001 0.000 HIS A 198 PHE 0.013 0.001 PHE L 87 TYR 0.022 0.001 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 78 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.504 Fit side-chains REVERT: A 184 ARG cc_start: 0.7574 (ttm110) cc_final: 0.7278 (ttp-170) REVERT: A 244 ASP cc_start: 0.7316 (t70) cc_final: 0.6990 (t70) REVERT: H 91 THR cc_start: 0.8698 (p) cc_final: 0.8395 (p) REVERT: L 45 LYS cc_start: 0.8398 (ttpp) cc_final: 0.8123 (mtpp) outliers start: 12 outliers final: 12 residues processed: 76 average time/residue: 0.1411 time to fit residues: 14.0846 Evaluate side-chains 74 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 146 VAL 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: 0.3980 chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 45 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.160023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133087 restraints weight = 5506.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.136719 restraints weight = 3370.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.139077 restraints weight = 2462.433| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3027 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= 0.176 Angle : 0.613 11.204 5827 Z= 0.299 Chirality : 0.043 0.159 648 Planarity : 0.004 0.045 743 Dihedral : 4.314 18.377 611 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.04 % Allowed : 13.48 % 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: -0.06 (0.39), residues: 506 helix: 0.77 (0.62), residues: 73 sheet: 0.28 (0.40), residues: 157 loop : -0.39 (0.41), residues: 276 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 0.009 0.001 PHE A 65 TYR 0.022 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: 1669.12 seconds wall clock time: 30 minutes 29.71 seconds (1829.71 seconds total)