Starting phenix.real_space_refine on Mon Sep 23 21:13:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6v_31482/09_2024/7f6v_31482.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6v_31482/09_2024/7f6v_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6v_31482/09_2024/7f6v_31482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6v_31482/09_2024/7f6v_31482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6v_31482/09_2024/7f6v_31482.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6v_31482/09_2024/7f6v_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-5461/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: 3.83, per 1000 atoms: 0.72 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: 1.54 Conformation dependent library (CDL) restraints added in 637.3 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: 0.38 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: 1.22 Time building geometry restraints manager: 1.69 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: 0.00 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: 0.960 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.680 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.980 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.621 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: 0.2235 time to fit residues: 43.1324 Evaluate side-chains 119 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 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 fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8757 (mtt) cc_final: 0.8463 (ppp) REVERT: A 238 TYR cc_start: 0.7802 (t80) cc_final: 0.7495 (t80) REVERT: A 319 LEU cc_start: 0.8894 (tt) cc_final: 0.8651 (tp) REVERT: B 31 ARG cc_start: 0.9212 (tmm160) cc_final: 0.8909 (ttp80) REVERT: B 87 MET cc_start: 0.8738 (mtt) cc_final: 0.8451 (ppp) REVERT: B 238 TYR cc_start: 0.7785 (t80) cc_final: 0.7446 (t80) REVERT: B 239 TYR cc_start: 0.7744 (t80) cc_final: 0.7261 (m-80) REVERT: B 319 LEU cc_start: 0.8897 (tt) cc_final: 0.8652 (tp) outliers start: 13 outliers final: 10 residues processed: 129 average time/residue: 0.1735 time to fit residues: 28.7031 Evaluate side-chains 113 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 31 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 38 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 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 30 HIS ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5470 Z= 0.184 Angle : 0.564 6.794 7404 Z= 0.287 Chirality : 0.034 0.125 796 Planarity : 0.004 0.032 904 Dihedral : 4.525 32.169 810 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.52 % Allowed : 18.84 % Favored : 77.64 % 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: 3.99 (0.35), residues: 618 helix: 3.47 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -3.88 (0.68), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 305 HIS 0.013 0.002 HIS A 330 PHE 0.018 0.001 PHE A 235 TYR 0.012 0.001 TYR A 171 ARG 0.007 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 128 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8790 (mtt) cc_final: 0.8485 (ppp) REVERT: A 237 GLN cc_start: 0.7263 (tm-30) cc_final: 0.7003 (tm-30) REVERT: A 319 LEU cc_start: 0.8875 (tt) cc_final: 0.8623 (tp) REVERT: B 87 MET cc_start: 0.8786 (mtt) cc_final: 0.8484 (ppp) REVERT: B 237 GLN cc_start: 0.7268 (tm-30) cc_final: 0.7001 (tm-30) REVERT: B 319 LEU cc_start: 0.8923 (tt) cc_final: 0.8675 (tp) outliers start: 20 outliers final: 14 residues processed: 117 average time/residue: 0.1504 time to fit residues: 23.3964 Evaluate side-chains 119 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 272 LEU Chi-restraints excluded: chain A residue 323 PHE 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 177 ILE Chi-restraints excluded: chain B residue 183 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 6.9990 chunk 42 optimal weight: 0.0870 chunk 29 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5470 Z= 0.178 Angle : 0.553 7.833 7404 Z= 0.276 Chirality : 0.033 0.122 796 Planarity : 0.004 0.038 904 Dihedral : 4.218 28.523 810 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.46 % Allowed : 22.01 % Favored : 75.53 % 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: 4.39 (0.34), residues: 618 helix: 3.66 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -2.63 (0.75), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 305 HIS 0.001 0.000 HIS A 30 PHE 0.020 0.001 PHE A 235 TYR 0.017 0.001 TYR B 238 ARG 0.009 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 125 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8807 (mtt) cc_final: 0.8343 (tmm) REVERT: A 203 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7323 (tp) REVERT: A 319 LEU cc_start: 0.8945 (tt) cc_final: 0.8701 (tp) REVERT: B 87 MET cc_start: 0.8812 (mtt) cc_final: 0.8331 (tmm) REVERT: B 319 LEU cc_start: 0.8947 (tt) cc_final: 0.8698 (tp) outliers start: 14 outliers final: 13 residues processed: 114 average time/residue: 0.1276 time to fit residues: 20.3852 Evaluate side-chains 116 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 203 LEU Chi-restraints excluded: chain A residue 239 TYR 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 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 244 CYS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 323 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 51 optimal weight: 0.0030 chunk 41 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5470 Z= 0.333 Angle : 0.670 8.030 7404 Z= 0.334 Chirality : 0.038 0.136 796 Planarity : 0.004 0.040 904 Dihedral : 4.270 16.471 810 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 5.46 % Allowed : 22.36 % 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: 4.15 (0.34), residues: 618 helix: 3.54 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -3.52 (0.70), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 210 HIS 0.004 0.001 HIS A 283 PHE 0.019 0.002 PHE A 219 TYR 0.015 0.002 TYR B 238 ARG 0.007 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 135 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 104 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8837 (mtt) cc_final: 0.8359 (tmm) REVERT: B 87 MET cc_start: 0.8831 (mtt) cc_final: 0.8347 (tmm) REVERT: B 197 HIS cc_start: 0.8532 (OUTLIER) cc_final: 0.8312 (m170) outliers start: 31 outliers final: 23 residues processed: 118 average time/residue: 0.1435 time to fit residues: 22.8454 Evaluate side-chains 126 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 35 LEU 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 239 TYR 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 32 LEU Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 35 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5470 Z= 0.211 Angle : 0.598 8.575 7404 Z= 0.295 Chirality : 0.035 0.131 796 Planarity : 0.003 0.028 904 Dihedral : 4.044 17.883 810 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % 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: 4.52 (0.35), residues: 618 helix: 3.74 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -2.53 (0.76), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 305 HIS 0.003 0.000 HIS A 283 PHE 0.022 0.001 PHE B 235 TYR 0.014 0.001 TYR A 238 ARG 0.005 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 130 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8808 (mtt) cc_final: 0.8342 (tmm) REVERT: A 237 GLN cc_start: 0.7214 (tm-30) cc_final: 0.6992 (tm-30) REVERT: A 319 LEU cc_start: 0.8963 (tt) cc_final: 0.8694 (tp) REVERT: B 87 MET cc_start: 0.8816 (mtt) cc_final: 0.8328 (tmm) REVERT: B 319 LEU cc_start: 0.8969 (tt) cc_final: 0.8699 (tp) REVERT: B 327 ARG cc_start: 0.7193 (tpt170) cc_final: 0.6979 (tpt170) outliers start: 24 outliers final: 16 residues processed: 120 average time/residue: 0.1371 time to fit residues: 22.3254 Evaluate side-chains 117 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 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 142 ILE Chi-restraints excluded: chain A residue 177 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5470 Z= 0.185 Angle : 0.619 12.315 7404 Z= 0.293 Chirality : 0.034 0.134 796 Planarity : 0.003 0.025 904 Dihedral : 3.948 19.584 810 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.70 % Allowed : 23.94 % 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: 4.65 (0.35), residues: 618 helix: 3.82 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -2.43 (0.77), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 305 HIS 0.002 0.000 HIS B 283 PHE 0.017 0.001 PHE B 219 TYR 0.013 0.001 TYR B 238 ARG 0.003 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 127 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.9236 (tmm160) cc_final: 0.9025 (ttp80) REVERT: A 87 MET cc_start: 0.8808 (mtt) cc_final: 0.8336 (tmm) REVERT: A 237 GLN cc_start: 0.7177 (tm-30) cc_final: 0.6917 (tm-30) REVERT: A 319 LEU cc_start: 0.8944 (tt) cc_final: 0.8678 (tp) REVERT: B 31 ARG cc_start: 0.9258 (tmm160) cc_final: 0.9038 (ttp80) REVERT: B 87 MET cc_start: 0.8805 (mtt) cc_final: 0.8322 (tmm) REVERT: B 237 GLN cc_start: 0.7177 (tm-30) cc_final: 0.6932 (tm-30) REVERT: B 319 LEU cc_start: 0.8967 (tt) cc_final: 0.8703 (tp) outliers start: 21 outliers final: 17 residues processed: 119 average time/residue: 0.1589 time to fit residues: 25.1018 Evaluate side-chains 120 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 209 THR 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 32 LEU Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 142 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 46 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4188 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= 0.164 Angle : 0.602 10.829 7404 Z= 0.285 Chirality : 0.036 0.266 796 Planarity : 0.003 0.025 904 Dihedral : 3.885 21.323 810 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.46 % Allowed : 25.18 % 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: 4.58 (0.35), residues: 618 helix: 3.77 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -2.39 (0.77), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 305 HIS 0.002 0.000 HIS B 283 PHE 0.025 0.001 PHE A 235 TYR 0.014 0.001 TYR B 238 ARG 0.003 0.001 ARG B 14 *********************** 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 116 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.9220 (tmm160) cc_final: 0.9011 (ttp80) REVERT: A 87 MET cc_start: 0.8805 (mtt) cc_final: 0.8326 (tmm) REVERT: A 237 GLN cc_start: 0.7218 (tm-30) cc_final: 0.6951 (tm-30) REVERT: A 319 LEU cc_start: 0.8959 (tt) cc_final: 0.8707 (tp) REVERT: A 334 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.7569 (t-170) REVERT: B 31 ARG cc_start: 0.9239 (tmm160) cc_final: 0.9023 (ttp80) REVERT: B 87 MET cc_start: 0.8801 (mtt) cc_final: 0.8312 (tmm) REVERT: B 237 GLN cc_start: 0.7171 (tm-30) cc_final: 0.6915 (tm-30) REVERT: B 319 LEU cc_start: 0.8978 (tt) cc_final: 0.8722 (tp) REVERT: B 334 HIS cc_start: 0.8129 (OUTLIER) cc_final: 0.7559 (t-170) outliers start: 14 outliers final: 11 residues processed: 111 average time/residue: 0.1411 time to fit residues: 21.1588 Evaluate side-chains 113 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 35 LEU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 314 PHE 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 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 24 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5470 Z= 0.182 Angle : 0.606 10.639 7404 Z= 0.288 Chirality : 0.037 0.275 796 Planarity : 0.003 0.026 904 Dihedral : 3.858 18.758 810 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.99 % Allowed : 24.65 % 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: 4.65 (0.35), residues: 618 helix: 3.81 (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 0.009 0.001 TRP A 193 HIS 0.002 0.000 HIS B 283 PHE 0.016 0.001 PHE B 219 TYR 0.026 0.001 TYR B 238 ARG 0.003 0.001 ARG B 14 *********************** 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 121 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.9218 (tmm160) cc_final: 0.9007 (ttp80) REVERT: A 87 MET cc_start: 0.8797 (mtt) cc_final: 0.8316 (tmm) REVERT: A 237 GLN cc_start: 0.7247 (tm-30) cc_final: 0.7005 (tm-30) REVERT: A 319 LEU cc_start: 0.8986 (tt) cc_final: 0.8732 (tp) REVERT: A 334 HIS cc_start: 0.8148 (OUTLIER) cc_final: 0.7533 (t-170) REVERT: B 31 ARG cc_start: 0.9246 (tmm160) cc_final: 0.9038 (ttp80) REVERT: B 87 MET cc_start: 0.8794 (mtt) cc_final: 0.8301 (tmm) REVERT: B 237 GLN cc_start: 0.7193 (tm-30) cc_final: 0.6895 (tm-30) REVERT: B 319 LEU cc_start: 0.9005 (tt) cc_final: 0.8746 (tp) REVERT: B 334 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.7573 (t-170) outliers start: 17 outliers final: 13 residues processed: 114 average time/residue: 0.1604 time to fit residues: 23.9611 Evaluate side-chains 114 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 35 LEU 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 35 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5470 Z= 0.177 Angle : 0.619 10.325 7404 Z= 0.297 Chirality : 0.036 0.229 796 Planarity : 0.003 0.025 904 Dihedral : 3.848 20.601 810 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.11 % Allowed : 24.82 % Favored : 73.06 % 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: 3.78 (0.21), residues: 532 sheet: None (None), residues: 0 loop : -2.39 (0.78), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 193 HIS 0.002 0.000 HIS B 283 PHE 0.024 0.001 PHE A 235 TYR 0.011 0.001 TYR B 171 ARG 0.003 0.000 ARG B 14 ********************** 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 116 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.9223 (tmm160) cc_final: 0.9022 (ttp80) REVERT: A 87 MET cc_start: 0.8797 (mtt) cc_final: 0.8303 (tmm) REVERT: A 237 GLN cc_start: 0.7234 (tm-30) cc_final: 0.6940 (tm-30) REVERT: A 319 LEU cc_start: 0.8971 (tt) cc_final: 0.8727 (tp) REVERT: A 334 HIS cc_start: 0.8134 (OUTLIER) cc_final: 0.7518 (t-170) REVERT: B 31 ARG cc_start: 0.9240 (tmm160) cc_final: 0.9033 (ttp80) REVERT: B 87 MET cc_start: 0.8809 (mtt) cc_final: 0.8306 (tmm) REVERT: B 237 GLN cc_start: 0.7217 (tm-30) cc_final: 0.6898 (tm-30) REVERT: B 319 LEU cc_start: 0.8993 (tt) cc_final: 0.8742 (tp) REVERT: B 334 HIS cc_start: 0.8129 (OUTLIER) cc_final: 0.7506 (t-170) outliers start: 12 outliers final: 8 residues processed: 114 average time/residue: 0.1434 time to fit residues: 22.0836 Evaluate side-chains 111 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 35 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 35 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 13 optimal weight: 0.9990 chunk 49 optimal weight: 0.0770 chunk 20 optimal weight: 0.1980 chunk 50 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.162426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.123509 restraints weight = 8956.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.127531 restraints weight = 4474.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.130067 restraints weight = 3087.367| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4761 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= 0.171 Angle : 0.605 10.092 7404 Z= 0.287 Chirality : 0.036 0.253 796 Planarity : 0.003 0.024 904 Dihedral : 3.810 20.865 810 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % 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: 4.61 (0.35), residues: 618 helix: 3.74 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -2.40 (0.80), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 193 HIS 0.002 0.000 HIS B 283 PHE 0.023 0.001 PHE A 235 TYR 0.024 0.001 TYR A 238 ARG 0.002 0.001 ARG B 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1312.16 seconds wall clock time: 24 minutes 5.70 seconds (1445.70 seconds total)