Starting phenix.real_space_refine on Thu Mar 6 07:49:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f6v_31482/03_2025/7f6v_31482.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f6v_31482/03_2025/7f6v_31482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f6v_31482/03_2025/7f6v_31482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f6v_31482/03_2025/7f6v_31482.map" model { file = "/net/cci-nas-00/data/ceres_data/7f6v_31482/03_2025/7f6v_31482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f6v_31482/03_2025/7f6v_31482.cif" } resolution = 3.66 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= 0.001 sd= 0.048 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 30 5.16 5 C 3526 2.51 5 N 866 2.21 5 O 892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5314 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2629 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2629 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.95, per 1000 atoms: 0.74 Number of scatterers: 5314 At special positions: 0 Unit cell: (94.302, 116.61, 92.274, 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 30 16.00 O 892 8.00 N 866 7.00 C 3526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 613.0 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 87.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 9 through 69 removed outlier: 3.562A pdb=" N ARG A 34 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU A 35 " --> pdb=" O ARG A 31 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 99 Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 122 through 154 Processing helix chain 'A' and resid 159 through 186 Processing helix chain 'A' and resid 192 through 210 removed outlier: 3.758A pdb=" N TYR A 198 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 248 removed outlier: 4.307A pdb=" N LYS A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 299 Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 303 through 334 Proline residue: A 313 - end of helix Processing helix chain 'B' and resid 9 through 69 removed outlier: 3.562A pdb=" N ARG B 34 " --> pdb=" O HIS B 30 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B 35 " --> pdb=" O ARG B 31 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 99 Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 122 through 154 Processing helix chain 'B' and resid 159 through 186 Processing helix chain 'B' and resid 192 through 210 removed outlier: 3.758A pdb=" N TYR B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 248 removed outlier: 4.307A pdb=" N LYS B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 299 Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 303 through 334 Proline residue: B 313 - end of helix 452 hydrogen bonds defined for protein. 1356 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: 1.31 Time building geometry restraints manager: 1.62 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: 1596 1.34 - 1.46: 1356 1.46 - 1.58: 2474 1.58 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 5470 Sorted by residual: bond pdb=" C10 CLR A 401 " pdb=" C9 CLR A 401 " ideal model delta sigma weight residual 1.551 1.520 0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C10 CLR B 401 " pdb=" C9 CLR B 401 " ideal model delta sigma weight residual 1.551 1.520 0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C5 CLR B 401 " pdb=" C6 CLR B 401 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.37e+00 bond pdb=" C5 CLR A 401 " pdb=" C6 CLR A 401 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C13 CLR A 401 " pdb=" C17 CLR A 401 " ideal model delta sigma weight residual 1.550 1.525 0.025 2.00e-02 2.50e+03 1.57e+00 ... (remaining 5465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 7161 1.86 - 3.72: 191 3.72 - 5.59: 40 5.59 - 7.45: 8 7.45 - 9.31: 4 Bond angle restraints: 7404 Sorted by residual: angle pdb=" C CYS A 68 " pdb=" N LYS A 69 " pdb=" CA LYS A 69 " ideal model delta sigma weight residual 119.78 123.78 -4.00 1.24e+00 6.50e-01 1.04e+01 angle pdb=" C CYS B 68 " pdb=" N LYS B 69 " pdb=" CA LYS B 69 " ideal model delta sigma weight residual 119.78 123.78 -4.00 1.24e+00 6.50e-01 1.04e+01 angle pdb=" C13 CLR A 401 " pdb=" C17 CLR A 401 " pdb=" C20 CLR A 401 " ideal model delta sigma weight residual 119.60 110.29 9.31 3.00e+00 1.11e-01 9.64e+00 angle pdb=" C13 CLR B 401 " pdb=" C17 CLR B 401 " pdb=" C20 CLR B 401 " ideal model delta sigma weight residual 119.60 110.33 9.27 3.00e+00 1.11e-01 9.54e+00 angle pdb=" C LYS B 69 " pdb=" CA LYS B 69 " pdb=" CB LYS B 69 " ideal model delta sigma weight residual 113.04 108.81 4.23 1.63e+00 3.76e-01 6.74e+00 ... (remaining 7399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 2954 17.67 - 35.34: 262 35.34 - 53.00: 42 53.00 - 70.67: 8 70.67 - 88.34: 4 Dihedral angle restraints: 3270 sinusoidal: 1422 harmonic: 1848 Sorted by residual: dihedral pdb=" CA LEU B 32 " pdb=" C LEU B 32 " pdb=" N TYR B 33 " pdb=" CA TYR B 33 " ideal model delta harmonic sigma weight residual -180.00 -163.61 -16.39 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA LEU A 32 " pdb=" C LEU A 32 " pdb=" N TYR A 33 " pdb=" CA TYR A 33 " ideal model delta harmonic sigma weight residual -180.00 -163.61 -16.39 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB GLU B 304 " pdb=" CG GLU B 304 " pdb=" CD GLU B 304 " pdb=" OE1 GLU B 304 " ideal model delta sinusoidal sigma weight residual 0.00 88.34 -88.34 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 3267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 772 0.105 - 0.210: 18 0.210 - 0.315: 2 0.315 - 0.420: 2 0.420 - 0.525: 2 Chirality restraints: 796 Sorted by residual: chirality pdb=" C14 CLR A 401 " pdb=" C13 CLR A 401 " pdb=" C15 CLR A 401 " pdb=" C8 CLR A 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.52 2.00e-01 2.50e+01 6.88e+00 chirality pdb=" C14 CLR B 401 " pdb=" C13 CLR B 401 " pdb=" C15 CLR B 401 " pdb=" C8 CLR B 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.52 2.00e-01 2.50e+01 6.77e+00 chirality pdb=" C10 CLR A 401 " pdb=" C1 CLR A 401 " pdb=" C5 CLR A 401 " pdb=" C9 CLR A 401 " both_signs ideal model delta sigma weight residual False -2.85 -2.49 -0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 793 not shown) Planarity restraints: 904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 313 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" C PRO B 313 " 0.025 2.00e-02 2.50e+03 pdb=" O PRO B 313 " -0.009 2.00e-02 2.50e+03 pdb=" N PHE B 314 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 313 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" C PRO A 313 " -0.025 2.00e-02 2.50e+03 pdb=" O PRO A 313 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE A 314 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 307 " 0.007 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C VAL A 307 " -0.022 2.00e-02 2.50e+03 pdb=" O VAL A 307 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU A 308 " 0.008 2.00e-02 2.50e+03 ... (remaining 901 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 1925 2.86 - 3.37: 5619 3.37 - 3.88: 8442 3.88 - 4.39: 8547 4.39 - 4.90: 14431 Nonbonded interactions: 38964 Sorted by model distance: nonbonded pdb=" O LYS B 332 " pdb=" OG SER B 335 " model vdw 2.356 3.040 nonbonded pdb=" O LYS A 332 " pdb=" OG SER A 335 " model vdw 2.356 3.040 nonbonded pdb=" OG SER B 157 " pdb=" NH1 ARG B 220 " model vdw 2.436 3.120 nonbonded pdb=" OG SER A 157 " pdb=" NH1 ARG A 220 " model vdw 2.436 3.120 nonbonded pdb=" O VAL B 159 " pdb=" N ALA B 162 " model vdw 2.443 3.120 ... (remaining 38959 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.510 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 : 0.005 0.039 5470 Z= 0.345 Angle : 0.774 9.312 7404 Z= 0.392 Chirality : 0.054 0.525 796 Planarity : 0.003 0.024 904 Dihedral : 13.915 88.339 2074 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % 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: 0.27 (0.32), residues: 618 helix: 0.94 (0.20), residues: 530 sheet: None (None), residues: 0 loop : -4.45 (0.59), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 193 HIS 0.002 0.001 HIS A 283 PHE 0.016 0.001 PHE A 219 TYR 0.016 0.002 TYR B 33 ARG 0.004 0.001 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.8727 (mtt) cc_final: 0.8420 (ppp) REVERT: A 145 ILE cc_start: 0.8404 (tt) cc_final: 0.8183 (tt) REVERT: A 154 LEU cc_start: 0.8208 (mm) cc_final: 0.7425 (tt) REVERT: A 228 MET cc_start: 0.8435 (ttt) cc_final: 0.7824 (ttm) REVERT: A 239 TYR cc_start: 0.8022 (t80) cc_final: 0.7550 (m-80) REVERT: B 87 MET cc_start: 0.8724 (mtt) cc_final: 0.8420 (ppp) REVERT: B 145 ILE cc_start: 0.8392 (tt) cc_final: 0.8168 (tt) REVERT: B 154 LEU cc_start: 0.8204 (mm) cc_final: 0.7428 (tt) REVERT: B 228 MET cc_start: 0.8434 (ttt) cc_final: 0.7817 (ttm) REVERT: B 239 TYR cc_start: 0.8015 (t80) cc_final: 0.7542 (m-80) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2211 time to fit residues: 42.8386 Evaluate side-chains 119 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 56 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 165 ASN A 241 GLN A 330 HIS B 165 ASN B 241 GLN B 330 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.158472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.118919 restraints weight = 8929.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.123080 restraints weight = 4270.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.125667 restraints weight = 2881.699| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5470 Z= 0.194 Angle : 0.602 6.077 7404 Z= 0.301 Chirality : 0.034 0.129 796 Planarity : 0.004 0.025 904 Dihedral : 5.165 34.194 810 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.29 % Allowed : 15.49 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.34), residues: 618 helix: 2.89 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -4.06 (0.65), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 305 HIS 0.009 0.001 HIS A 330 PHE 0.019 0.001 PHE B 235 TYR 0.011 0.001 TYR B 171 ARG 0.008 0.001 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8725 (mtt) cc_final: 0.8454 (ppp) REVERT: A 238 TYR cc_start: 0.7915 (t80) cc_final: 0.7592 (t80) REVERT: A 319 LEU cc_start: 0.8952 (tt) cc_final: 0.8689 (tp) REVERT: B 31 ARG cc_start: 0.9133 (tmm160) cc_final: 0.8853 (ttp80) REVERT: B 87 MET cc_start: 0.8716 (mtt) cc_final: 0.8446 (ppp) REVERT: B 238 TYR cc_start: 0.7909 (t80) cc_final: 0.7565 (t80) REVERT: B 239 TYR cc_start: 0.7714 (t80) cc_final: 0.7283 (m-80) REVERT: B 319 LEU cc_start: 0.8954 (tt) cc_final: 0.8691 (tp) outliers start: 13 outliers final: 10 residues processed: 129 average time/residue: 0.1669 time to fit residues: 27.6292 Evaluate side-chains 113 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 330 HIS Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 330 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 1 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 330 HIS ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.157788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.118082 restraints weight = 9104.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.122110 restraints weight = 4410.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.124630 restraints weight = 2997.262| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5470 Z= 0.253 Angle : 0.611 6.531 7404 Z= 0.310 Chirality : 0.036 0.122 796 Planarity : 0.004 0.044 904 Dihedral : 4.537 27.485 810 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.17 % Allowed : 20.25 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.35), residues: 618 helix: 3.36 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -3.91 (0.67), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 305 HIS 0.010 0.001 HIS A 330 PHE 0.017 0.002 PHE B 219 TYR 0.012 0.001 TYR B 171 ARG 0.006 0.001 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8779 (mtt) cc_final: 0.8311 (tmm) REVERT: A 237 GLN cc_start: 0.7315 (tm-30) cc_final: 0.7047 (tm-30) REVERT: A 238 TYR cc_start: 0.7996 (t80) cc_final: 0.7764 (t80) REVERT: A 319 LEU cc_start: 0.8976 (tt) cc_final: 0.8702 (tp) REVERT: B 87 MET cc_start: 0.8777 (mtt) cc_final: 0.8315 (tmm) REVERT: B 237 GLN cc_start: 0.7331 (tm-30) cc_final: 0.7053 (tm-30) REVERT: B 238 TYR cc_start: 0.7965 (t80) cc_final: 0.7747 (t80) REVERT: B 319 LEU cc_start: 0.9010 (tt) cc_final: 0.8748 (tp) outliers start: 18 outliers final: 14 residues processed: 118 average time/residue: 0.1596 time to fit residues: 24.7862 Evaluate side-chains 120 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 330 HIS Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 41 optimal weight: 0.0870 chunk 20 optimal weight: 0.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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 = 0.4280 r_free = 0.4280 target = 0.158877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.119525 restraints weight = 9249.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.123634 restraints weight = 4373.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.126156 restraints weight = 2944.402| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5470 Z= 0.193 Angle : 0.562 7.740 7404 Z= 0.284 Chirality : 0.034 0.124 796 Planarity : 0.004 0.038 904 Dihedral : 4.297 26.560 810 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.05 % Allowed : 21.65 % Favored : 74.30 % 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: 4.20 (0.35), residues: 618 helix: 3.59 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -3.63 (0.69), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 305 HIS 0.010 0.001 HIS A 330 PHE 0.017 0.001 PHE B 219 TYR 0.012 0.001 TYR B 171 ARG 0.007 0.001 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8773 (mtt) cc_final: 0.8327 (tmm) REVERT: A 238 TYR cc_start: 0.7907 (t80) cc_final: 0.7662 (t80) REVERT: A 319 LEU cc_start: 0.9002 (tt) cc_final: 0.8728 (tp) REVERT: B 87 MET cc_start: 0.8775 (mtt) cc_final: 0.8323 (tmm) REVERT: B 238 TYR cc_start: 0.7876 (t80) cc_final: 0.7642 (t80) REVERT: B 319 LEU cc_start: 0.8979 (tt) cc_final: 0.8706 (tp) outliers start: 23 outliers final: 18 residues processed: 116 average time/residue: 0.1238 time to fit residues: 20.2198 Evaluate side-chains 118 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.159479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.120537 restraints weight = 9121.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.124728 restraints weight = 4319.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.127332 restraints weight = 2894.618| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5470 Z= 0.189 Angle : 0.567 8.174 7404 Z= 0.283 Chirality : 0.034 0.126 796 Planarity : 0.004 0.044 904 Dihedral : 4.077 22.926 810 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.35 % Allowed : 22.89 % Favored : 73.77 % 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: 4.54 (0.35), residues: 618 helix: 3.76 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -2.56 (0.75), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 305 HIS 0.001 0.000 HIS A 30 PHE 0.020 0.001 PHE A 235 TYR 0.012 0.001 TYR B 171 ARG 0.008 0.001 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9425 (tmtt) cc_final: 0.9216 (tmtt) REVERT: A 87 MET cc_start: 0.8782 (mtt) cc_final: 0.8334 (tmm) REVERT: A 197 HIS cc_start: 0.8427 (OUTLIER) cc_final: 0.8184 (m170) REVERT: A 319 LEU cc_start: 0.8996 (tt) cc_final: 0.8723 (tp) REVERT: B 56 LYS cc_start: 0.9427 (tmtt) cc_final: 0.9216 (tmtt) REVERT: B 87 MET cc_start: 0.8779 (mtt) cc_final: 0.8325 (tmm) REVERT: B 319 LEU cc_start: 0.8986 (tt) cc_final: 0.8708 (tp) outliers start: 19 outliers final: 16 residues processed: 116 average time/residue: 0.1500 time to fit residues: 23.2276 Evaluate side-chains 121 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.161395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.122226 restraints weight = 9094.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.126432 restraints weight = 4294.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.128954 restraints weight = 2895.943| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5470 Z= 0.170 Angle : 0.566 8.678 7404 Z= 0.277 Chirality : 0.033 0.129 796 Planarity : 0.003 0.041 904 Dihedral : 3.875 21.574 810 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.23 % Allowed : 23.77 % Favored : 72.01 % 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: 4.69 (0.35), residues: 618 helix: 3.85 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -2.45 (0.77), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 305 HIS 0.001 0.000 HIS A 30 PHE 0.022 0.001 PHE B 235 TYR 0.020 0.001 TYR B 238 ARG 0.009 0.001 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8783 (mtt) cc_final: 0.8314 (tmm) REVERT: A 319 LEU cc_start: 0.8921 (tt) cc_final: 0.8658 (tp) REVERT: A 327 ARG cc_start: 0.7187 (tpt170) cc_final: 0.6960 (tpt170) REVERT: B 87 MET cc_start: 0.8781 (mtt) cc_final: 0.8303 (tmm) REVERT: B 197 HIS cc_start: 0.8393 (OUTLIER) cc_final: 0.8186 (m170) REVERT: B 319 LEU cc_start: 0.8947 (tt) cc_final: 0.8677 (tp) outliers start: 24 outliers final: 14 residues processed: 126 average time/residue: 0.1579 time to fit residues: 26.3478 Evaluate side-chains 112 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 60 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4307 r_free = 0.4307 target = 0.161138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.122143 restraints weight = 9086.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.126330 restraints weight = 4319.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.128888 restraints weight = 2908.616| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5470 Z= 0.186 Angle : 0.629 11.786 7404 Z= 0.296 Chirality : 0.037 0.303 796 Planarity : 0.003 0.036 904 Dihedral : 3.885 19.735 810 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.29 % Allowed : 24.82 % Favored : 72.89 % 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: 4.62 (0.35), residues: 618 helix: 3.80 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -2.41 (0.77), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 305 HIS 0.003 0.001 HIS B 283 PHE 0.024 0.001 PHE A 235 TYR 0.021 0.001 TYR A 238 ARG 0.007 0.001 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8770 (mtt) cc_final: 0.8314 (tmm) REVERT: A 237 GLN cc_start: 0.7120 (tm-30) cc_final: 0.6868 (tm-30) REVERT: A 319 LEU cc_start: 0.9031 (tt) cc_final: 0.8750 (tp) REVERT: A 327 ARG cc_start: 0.7229 (tpt170) cc_final: 0.7027 (tpt170) REVERT: B 87 MET cc_start: 0.8769 (mtt) cc_final: 0.8305 (tmm) REVERT: B 237 GLN cc_start: 0.7117 (tm-30) cc_final: 0.6862 (tm-30) REVERT: B 319 LEU cc_start: 0.9033 (tt) cc_final: 0.8747 (tp) outliers start: 13 outliers final: 12 residues processed: 110 average time/residue: 0.1475 time to fit residues: 21.9903 Evaluate side-chains 112 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 32 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4304 r_free = 0.4304 target = 0.160890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.121928 restraints weight = 9103.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.126040 restraints weight = 4324.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.128590 restraints weight = 2918.162| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5470 Z= 0.183 Angle : 0.622 11.072 7404 Z= 0.291 Chirality : 0.036 0.245 796 Planarity : 0.004 0.047 904 Dihedral : 3.829 18.870 810 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.64 % Allowed : 24.47 % Favored : 72.89 % 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: 4.64 (0.35), residues: 618 helix: 3.81 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -2.37 (0.77), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 305 HIS 0.002 0.000 HIS A 283 PHE 0.015 0.001 PHE B 219 TYR 0.019 0.001 TYR B 238 ARG 0.011 0.001 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8777 (mtt) cc_final: 0.8313 (tmm) REVERT: A 284 PHE cc_start: 0.7636 (m-10) cc_final: 0.7391 (m-80) REVERT: A 319 LEU cc_start: 0.9044 (tt) cc_final: 0.8773 (tp) REVERT: A 334 HIS cc_start: 0.7987 (OUTLIER) cc_final: 0.7430 (t-170) REVERT: B 87 MET cc_start: 0.8779 (mtt) cc_final: 0.8305 (tmm) REVERT: B 319 LEU cc_start: 0.9023 (tt) cc_final: 0.8757 (tp) REVERT: B 334 HIS cc_start: 0.7993 (OUTLIER) cc_final: 0.7375 (t-170) outliers start: 15 outliers final: 11 residues processed: 108 average time/residue: 0.1451 time to fit residues: 21.1549 Evaluate side-chains 109 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 58 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.161268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.122364 restraints weight = 8519.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.126362 restraints weight = 4182.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.128842 restraints weight = 2850.479| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5470 Z= 0.186 Angle : 0.628 10.351 7404 Z= 0.295 Chirality : 0.036 0.221 796 Planarity : 0.004 0.036 904 Dihedral : 3.768 19.688 810 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.11 % Allowed : 25.53 % Favored : 72.36 % 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: 4.66 (0.35), residues: 618 helix: 3.78 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -2.44 (0.79), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 305 HIS 0.002 0.000 HIS B 283 PHE 0.023 0.001 PHE A 235 TYR 0.017 0.001 TYR A 238 ARG 0.009 0.001 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8707 (mtt) cc_final: 0.8260 (tmm) REVERT: A 319 LEU cc_start: 0.9048 (tt) cc_final: 0.8781 (tp) REVERT: A 334 HIS cc_start: 0.7968 (OUTLIER) cc_final: 0.7344 (t-170) REVERT: B 87 MET cc_start: 0.8715 (mtt) cc_final: 0.8257 (tmm) REVERT: B 319 LEU cc_start: 0.9045 (tt) cc_final: 0.8777 (tp) REVERT: B 334 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.7279 (t-170) outliers start: 12 outliers final: 9 residues processed: 108 average time/residue: 0.1421 time to fit residues: 20.9049 Evaluate side-chains 110 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.4251 r_free = 0.4251 target = 0.156143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.116695 restraints weight = 9072.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.120656 restraints weight = 4509.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.123065 restraints weight = 3088.806| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5470 Z= 0.242 Angle : 0.670 10.828 7404 Z= 0.316 Chirality : 0.038 0.217 796 Planarity : 0.004 0.035 904 Dihedral : 3.913 17.569 810 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.46 % Allowed : 25.35 % Favored : 72.18 % 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: 4.63 (0.35), residues: 618 helix: 3.82 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -2.23 (0.74), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 305 HIS 0.002 0.000 HIS A 283 PHE 0.021 0.002 PHE A 235 TYR 0.018 0.002 TYR A 238 ARG 0.009 0.001 ARG A 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8792 (mtt) cc_final: 0.8314 (tmm) REVERT: A 188 ARG cc_start: 0.7582 (ppt170) cc_final: 0.7361 (ppt170) REVERT: B 87 MET cc_start: 0.8790 (mtt) cc_final: 0.8307 (tmm) outliers start: 14 outliers final: 13 residues processed: 107 average time/residue: 0.1237 time to fit residues: 18.6003 Evaluate side-chains 111 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 12 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 38 optimal weight: 9.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- 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 = 0.4291 r_free = 0.4291 target = 0.159553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.120324 restraints weight = 9065.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.124374 restraints weight = 4474.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.126864 restraints weight = 3070.227| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5470 Z= 0.181 Angle : 0.625 10.168 7404 Z= 0.293 Chirality : 0.036 0.211 796 Planarity : 0.004 0.032 904 Dihedral : 3.779 20.251 810 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.46 % Allowed : 26.23 % Favored : 71.30 % 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: 4.70 (0.35), residues: 618 helix: 3.84 (0.21), residues: 532 sheet: None (None), residues: 0 loop : -2.49 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 305 HIS 0.003 0.000 HIS A 283 PHE 0.024 0.001 PHE A 235 TYR 0.016 0.001 TYR A 238 ARG 0.008 0.001 ARG A 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1820.87 seconds wall clock time: 32 minutes 23.82 seconds (1943.82 seconds total)