Starting phenix.real_space_refine (version: dev) on Fri Feb 17 15:19:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6v_31482/02_2023/7f6v_31482_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6v_31482/02_2023/7f6v_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_31482/02_2023/7f6v_31482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6v_31482/02_2023/7f6v_31482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6v_31482/02_2023/7f6v_31482_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6v_31482/02_2023/7f6v_31482_updated.pdb" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 3.34, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 1.83 Conformation dependent library (CDL) restraints added in 670.3 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... running ksdssp... Secondary structure from input PDB file: 18 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 10 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 78 through 100 removed outlier: 4.005A pdb=" N TYR A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 123 through 153 Processing helix chain 'A' and resid 160 through 185 Processing helix chain 'A' and resid 193 through 209 removed outlier: 3.758A pdb=" N TYR A 198 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 247 Processing helix chain 'A' and resid 265 through 298 Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 304 through 333 Proline residue: A 313 - end of helix Processing helix chain 'B' and resid 10 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 78 through 100 removed outlier: 4.005A pdb=" N TYR B 100 " --> pdb=" O ASP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 112 Processing helix chain 'B' and resid 123 through 153 Processing helix chain 'B' and resid 160 through 185 Processing helix chain 'B' and resid 193 through 209 removed outlier: 3.758A pdb=" N TYR B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 247 Processing helix chain 'B' and resid 265 through 298 Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 304 through 333 Proline residue: B 313 - end of helix 424 hydrogen bonds defined for protein. 1272 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: 1.33 Time building geometry restraints manager: 2.01 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: 100.34 - 107.07: 120 107.07 - 113.80: 3062 113.80 - 120.53: 2336 120.53 - 127.26: 1822 127.26 - 133.98: 64 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: 2844 17.67 - 35.34: 260 35.34 - 53.00: 42 53.00 - 70.67: 8 70.67 - 88.34: 4 Dihedral angle restraints: 3158 sinusoidal: 1310 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 3155 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: 1929 2.86 - 3.37: 5635 3.37 - 3.88: 8482 3.88 - 4.39: 8583 4.39 - 4.90: 14447 Nonbonded interactions: 39076 Sorted by model distance: nonbonded pdb=" O LYS B 332 " pdb=" OG SER B 335 " model vdw 2.356 2.440 nonbonded pdb=" O LYS A 332 " pdb=" OG SER A 335 " model vdw 2.356 2.440 nonbonded pdb=" OG SER B 157 " pdb=" NH1 ARG B 220 " model vdw 2.436 2.520 nonbonded pdb=" OG SER A 157 " pdb=" NH1 ARG A 220 " model vdw 2.436 2.520 nonbonded pdb=" O VAL B 159 " pdb=" N ALA B 162 " model vdw 2.443 2.520 ... (remaining 39071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 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. 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: 0.730 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: 3.280 Check model and map are aligned: 0.080 Process input model: 16.240 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.050 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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= 0.347 Angle : 0.774 9.312 7404 Z= 0.392 Chirality : 0.054 0.525 796 Planarity : 0.003 0.024 904 Dihedral : 14.140 88.339 1962 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 % 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 *********************** 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 : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2380 time to fit residues: 46.3211 Evaluate side-chains 119 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.596 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7760 ------------------------------------------------------------------------------- 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: 0.7980 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 330 HIS B 241 GLN B 330 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2488 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= 0.204 Angle : 0.606 5.859 7404 Z= 0.298 Chirality : 0.034 0.141 796 Planarity : 0.003 0.026 904 Dihedral : 4.301 31.915 698 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 2.64 % 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: 2.85 (0.35), residues: 618 helix: 2.75 (0.21), residues: 532 sheet: None (None), residues: 0 loop : -4.25 (0.63), residues: 86 *********************** 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 137 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 128 average time/residue: 0.1798 time to fit residues: 29.6175 Evaluate side-chains 111 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 0.654 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0584 time to fit residues: 1.6718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 5470 Z= 0.225 Angle : 0.600 6.679 7404 Z= 0.299 Chirality : 0.035 0.124 796 Planarity : 0.004 0.040 904 Dihedral : 4.113 30.673 698 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 2.29 % 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: 3.76 (0.35), residues: 618 helix: 3.30 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -3.00 (0.76), residues: 92 *********************** 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 129 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 122 average time/residue: 0.1466 time to fit residues: 23.8974 Evaluate side-chains 116 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 0.557 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0512 time to fit residues: 1.7107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.0060 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3416 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= 0.171 Angle : 0.555 8.009 7404 Z= 0.274 Chirality : 0.032 0.121 796 Planarity : 0.004 0.034 904 Dihedral : 3.955 35.252 698 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.12 (0.35), residues: 618 helix: 3.54 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -2.86 (0.75), residues: 92 *********************** 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 120 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 120 average time/residue: 0.1577 time to fit residues: 25.1450 Evaluate side-chains 105 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.630 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3474 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= 0.222 Angle : 0.602 8.359 7404 Z= 0.293 Chirality : 0.034 0.132 796 Planarity : 0.004 0.043 904 Dihedral : 3.900 28.283 698 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.24 (0.35), residues: 618 helix: 3.58 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -2.64 (0.76), residues: 90 *********************** 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 130 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 126 average time/residue: 0.1647 time to fit residues: 28.1568 Evaluate side-chains 120 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 0.704 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0543 time to fit residues: 1.8758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 49 optimal weight: 0.0970 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 0.0030 chunk 57 optimal weight: 0.8980 chunk 6 optimal weight: 0.0770 chunk 34 optimal weight: 3.9990 overall best weight: 0.3946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS B 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 5470 Z= 0.154 Angle : 0.611 12.021 7404 Z= 0.280 Chirality : 0.032 0.119 796 Planarity : 0.004 0.047 904 Dihedral : 3.831 30.995 698 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer Outliers : 1.58 % 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: 4.38 (0.35), residues: 618 helix: 3.70 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -2.64 (0.77), residues: 92 *********************** 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 121 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 120 average time/residue: 0.1676 time to fit residues: 26.8532 Evaluate side-chains 98 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 0.696 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0651 time to fit residues: 1.1486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7687 moved from start: 0.4104 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= 0.183 Angle : 0.628 10.053 7404 Z= 0.296 Chirality : 0.036 0.299 796 Planarity : 0.003 0.034 904 Dihedral : 3.736 24.248 698 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 0.53 % 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: 4.34 (0.35), residues: 618 helix: 3.62 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -2.42 (0.77), residues: 90 *********************** 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 106 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 104 average time/residue: 0.1631 time to fit residues: 22.3261 Evaluate side-chains 104 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.592 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0501 time to fit residues: 0.9460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.0010 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.0470 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7486 ------------------------------------------------------------------------------- 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: 0.7683 moved from start: 0.4255 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= 0.173 Angle : 0.608 9.171 7404 Z= 0.286 Chirality : 0.035 0.271 796 Planarity : 0.004 0.053 904 Dihedral : 3.694 22.631 698 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 0.53 % 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: 4.37 (0.35), residues: 618 helix: 3.62 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -2.25 (0.79), residues: 90 *********************** 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 107 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 107 average time/residue: 0.1530 time to fit residues: 21.9682 Evaluate side-chains 105 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 0.569 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0563 time to fit residues: 1.1458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.0570 chunk 43 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.1980 chunk 36 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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: 0.7630 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 5470 Z= 0.157 Angle : 0.606 8.805 7404 Z= 0.284 Chirality : 0.034 0.226 796 Planarity : 0.003 0.034 904 Dihedral : 3.596 25.208 698 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.40 (0.35), residues: 618 helix: 3.62 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -2.07 (0.80), residues: 90 *********************** 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 108 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 107 average time/residue: 0.1513 time to fit residues: 21.8384 Evaluate side-chains 102 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.636 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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: 0.7653 moved from start: 0.4601 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= 0.175 Angle : 0.638 8.782 7404 Z= 0.302 Chirality : 0.035 0.212 796 Planarity : 0.004 0.033 904 Dihedral : 3.648 21.550 698 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.18 % 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: 4.33 (0.35), residues: 618 helix: 3.54 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -1.96 (0.81), residues: 90 ********************** 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 101 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.1119 time to fit residues: 16.4690 Evaluate side-chains 99 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.637 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 20 optimal weight: 0.0770 chunk 50 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 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 = 0.4332 r_free = 0.4332 target = 0.162616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.124477 restraints weight = 8986.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.128438 restraints weight = 4443.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.130861 restraints weight = 3056.833| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 5470 Z= 0.171 Angle : 0.631 8.558 7404 Z= 0.297 Chirality : 0.034 0.214 796 Planarity : 0.003 0.031 904 Dihedral : 3.681 20.641 698 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.00 % 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: 4.28 (0.35), residues: 618 helix: 3.50 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -1.91 (0.81), residues: 90 =============================================================================== Job complete usr+sys time: 1298.66 seconds wall clock time: 24 minutes 27.15 seconds (1467.15 seconds total)