Starting phenix.real_space_refine on Thu Jul 18 22:00:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1z_36806/07_2024/8k1z_36806.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1z_36806/07_2024/8k1z_36806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1z_36806/07_2024/8k1z_36806.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1z_36806/07_2024/8k1z_36806.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1z_36806/07_2024/8k1z_36806.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1z_36806/07_2024/8k1z_36806.cif" } resolution = 3.41 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= 0.074 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: 5 Type Number sf(0) Gaussians K 5 8.98 5 S 32 5.16 5 C 2706 2.51 5 N 616 2.21 5 O 700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 183": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4059 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1921 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain breaks: 1 Chain: "B" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1921 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain breaks: 1 Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 109 Unusual residues: {' K': 4, 'Y01': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {' K': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.99, per 1000 atoms: 0.74 Number of scatterers: 4059 At special positions: 0 Unit cell: (64.9, 73.7, 89.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 5 19.00 S 32 16.00 O 700 8.00 N 616 7.00 C 2706 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=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 692.8 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 896 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 87.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 2 through 53 removed outlier: 5.621A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N HIS A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 removed outlier: 3.707A pdb=" N ARG A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 103 through 147 Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 155 through 183 removed outlier: 3.791A pdb=" N GLU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 217 through 241 removed outlier: 3.511A pdb=" N ASN A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.611A pdb=" N THR A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 53 removed outlier: 5.619A pdb=" N ASP B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N HIS B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 70 removed outlier: 3.680A pdb=" N ARG B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 103 through 147 Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 155 through 180 Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 248 removed outlier: 4.307A pdb=" N ARG B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 972 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: 1.03 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 673 1.33 - 1.45: 1085 1.45 - 1.57: 2350 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 4156 Sorted by residual: bond pdb=" CA MET A 156 " pdb=" C MET A 156 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.26e-02 6.30e+03 1.17e+01 bond pdb=" CA GLU B 157 " pdb=" C GLU B 157 " ideal model delta sigma weight residual 1.524 1.486 0.038 1.29e-02 6.01e+03 8.55e+00 bond pdb=" C GLU B 157 " pdb=" N ASN B 158 " ideal model delta sigma weight residual 1.335 1.296 0.039 1.36e-02 5.41e+03 8.03e+00 bond pdb=" N MET A 156 " pdb=" CA MET A 156 " ideal model delta sigma weight residual 1.459 1.425 0.034 1.20e-02 6.94e+03 7.97e+00 bond pdb=" C MET A 156 " pdb=" N GLU A 157 " ideal model delta sigma weight residual 1.335 1.310 0.025 1.30e-02 5.92e+03 3.81e+00 ... (remaining 4151 not shown) Histogram of bond angle deviations from ideal: 99.96 - 106.76: 91 106.76 - 113.57: 2281 113.57 - 120.37: 1587 120.37 - 127.18: 1661 127.18 - 133.98: 24 Bond angle restraints: 5644 Sorted by residual: angle pdb=" N VAL A 242 " pdb=" CA VAL A 242 " pdb=" C VAL A 242 " ideal model delta sigma weight residual 113.71 109.72 3.99 9.50e-01 1.11e+00 1.76e+01 angle pdb=" N MET A 156 " pdb=" CA MET A 156 " pdb=" C MET A 156 " ideal model delta sigma weight residual 111.14 107.73 3.41 1.08e+00 8.57e-01 9.95e+00 angle pdb=" C SER A 155 " pdb=" N MET A 156 " pdb=" CA MET A 156 " ideal model delta sigma weight residual 120.44 116.32 4.12 1.36e+00 5.41e-01 9.20e+00 angle pdb=" N VAL A 243 " pdb=" CA VAL A 243 " pdb=" C VAL A 243 " ideal model delta sigma weight residual 112.12 110.12 2.00 8.40e-01 1.42e+00 5.65e+00 angle pdb=" C LYS A 2 " pdb=" CA LYS A 2 " pdb=" CB LYS A 2 " ideal model delta sigma weight residual 110.10 114.41 -4.31 1.90e+00 2.77e-01 5.13e+00 ... (remaining 5639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 2396 16.09 - 32.18: 238 32.18 - 48.27: 55 48.27 - 64.36: 15 64.36 - 80.44: 8 Dihedral angle restraints: 2712 sinusoidal: 1310 harmonic: 1402 Sorted by residual: dihedral pdb=" CG ARG A 7 " pdb=" CD ARG A 7 " pdb=" NE ARG A 7 " pdb=" CZ ARG A 7 " ideal model delta sinusoidal sigma weight residual 90.00 130.50 -40.50 2 1.50e+01 4.44e-03 9.00e+00 dihedral pdb=" CB GLU B 130 " pdb=" CG GLU B 130 " pdb=" CD GLU B 130 " pdb=" OE1 GLU B 130 " ideal model delta sinusoidal sigma weight residual 0.00 79.79 -79.79 1 3.00e+01 1.11e-03 8.78e+00 dihedral pdb=" CB GLU A 130 " pdb=" CG GLU A 130 " pdb=" CD GLU A 130 " pdb=" OE1 GLU A 130 " ideal model delta sinusoidal sigma weight residual 0.00 79.69 -79.69 1 3.00e+01 1.11e-03 8.76e+00 ... (remaining 2709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 450 0.022 - 0.043: 72 0.043 - 0.065: 86 0.065 - 0.087: 27 0.087 - 0.108: 15 Chirality restraints: 650 Sorted by residual: chirality pdb=" CA VAL B 76 " pdb=" N VAL B 76 " pdb=" C VAL B 76 " pdb=" CB VAL B 76 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.94e-01 chirality pdb=" CA VAL A 76 " pdb=" N VAL A 76 " pdb=" C VAL A 76 " pdb=" CB VAL A 76 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.79e-01 chirality pdb=" CA VAL A 206 " pdb=" N VAL A 206 " pdb=" C VAL A 206 " pdb=" CB VAL A 206 " both_signs ideal model delta sigma weight residual False 2.44 2.54 -0.10 2.00e-01 2.50e+01 2.58e-01 ... (remaining 647 not shown) Planarity restraints: 664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 2 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C LYS A 2 " 0.033 2.00e-02 2.50e+03 pdb=" O LYS A 2 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG A 3 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 156 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" C MET B 156 " 0.028 2.00e-02 2.50e+03 pdb=" O MET B 156 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU B 157 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 156 " 0.005 2.00e-02 2.50e+03 9.51e-03 9.05e-01 pdb=" C MET A 156 " -0.016 2.00e-02 2.50e+03 pdb=" O MET A 156 " 0.006 2.00e-02 2.50e+03 pdb=" N GLU A 157 " 0.006 2.00e-02 2.50e+03 ... (remaining 661 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 1154 2.82 - 3.40: 4506 3.40 - 3.98: 7281 3.98 - 4.56: 10210 4.56 - 5.14: 14419 Nonbonded interactions: 37570 Sorted by model distance: nonbonded pdb=" OG SER B 179 " pdb=" O TRP B 184 " model vdw 2.241 2.440 nonbonded pdb=" OE1 GLN A 126 " pdb=" ND2 ASN A 240 " model vdw 2.246 2.520 nonbonded pdb=" OH TYR A 52 " pdb=" OD2 ASP B 58 " model vdw 2.302 2.440 nonbonded pdb=" OG SER A 179 " pdb=" O TRP A 184 " model vdw 2.303 2.440 nonbonded pdb=" OD2 ASP A 58 " pdb=" OH TYR B 52 " model vdw 2.313 2.440 ... (remaining 37565 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' and (resid 2 through 248 or resid 301 through 304)) 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 individual isotropic 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.860 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 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 : 0.002 0.043 4156 Z= 0.119 Angle : 0.420 4.902 5644 Z= 0.247 Chirality : 0.032 0.108 650 Planarity : 0.002 0.019 664 Dihedral : 13.664 80.444 1816 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: 5.04 (0.38), residues: 476 helix: 3.84 (0.25), residues: 394 sheet: None (None), residues: 0 loop : 0.42 (0.71), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 184 HIS 0.001 0.000 HIS A 98 PHE 0.004 0.000 PHE B 109 TYR 0.007 0.001 TYR B 18 ARG 0.001 0.000 ARG B 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.6915 (m-80) cc_final: 0.6458 (t80) REVERT: A 42 LYS cc_start: 0.8425 (ttmm) cc_final: 0.8046 (tppt) REVERT: A 47 ARG cc_start: 0.7749 (ttp80) cc_final: 0.7485 (ttp80) REVERT: A 111 MET cc_start: 0.7869 (mtm) cc_final: 0.7653 (mtp) REVERT: A 135 PHE cc_start: 0.7010 (t80) cc_final: 0.5929 (m-10) REVERT: B 16 PHE cc_start: 0.6839 (m-80) cc_final: 0.6434 (t80) REVERT: B 42 LYS cc_start: 0.8426 (ttmm) cc_final: 0.8030 (tppt) REVERT: B 47 ARG cc_start: 0.7655 (ttp80) cc_final: 0.7448 (ttp80) REVERT: B 111 MET cc_start: 0.7910 (mtm) cc_final: 0.7710 (mtp) REVERT: B 135 PHE cc_start: 0.7018 (t80) cc_final: 0.5917 (m-10) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2206 time to fit residues: 27.1192 Evaluate side-chains 80 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.7868 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4156 Z= 0.248 Angle : 0.574 5.969 5644 Z= 0.301 Chirality : 0.039 0.137 650 Planarity : 0.004 0.042 664 Dihedral : 5.540 39.441 952 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.96 % Allowed : 9.07 % Favored : 88.97 % 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: 5.14 (0.40), residues: 476 helix: 3.84 (0.25), residues: 400 sheet: None (None), residues: 0 loop : 0.55 (0.83), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 184 HIS 0.002 0.001 HIS B 188 PHE 0.013 0.002 PHE B 223 TYR 0.025 0.002 TYR A 85 ARG 0.010 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.7560 (m-80) cc_final: 0.6469 (t80) REVERT: A 47 ARG cc_start: 0.7624 (ttp80) cc_final: 0.7265 (ttp80) REVERT: A 135 PHE cc_start: 0.7246 (t80) cc_final: 0.6105 (m-10) REVERT: B 16 PHE cc_start: 0.7477 (m-80) cc_final: 0.6457 (t80) REVERT: B 38 GLU cc_start: 0.8093 (tp30) cc_final: 0.7816 (tp30) REVERT: B 42 LYS cc_start: 0.8256 (ttmm) cc_final: 0.8047 (tppt) REVERT: B 47 ARG cc_start: 0.7647 (ttp80) cc_final: 0.7249 (ttp80) REVERT: B 135 PHE cc_start: 0.7227 (t80) cc_final: 0.6095 (m-10) outliers start: 8 outliers final: 2 residues processed: 100 average time/residue: 0.2079 time to fit residues: 24.6104 Evaluate side-chains 89 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 215 GLN B 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4156 Z= 0.219 Angle : 0.528 6.824 5644 Z= 0.274 Chirality : 0.036 0.132 650 Planarity : 0.003 0.019 664 Dihedral : 4.952 36.622 952 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.21 % Allowed : 14.46 % Favored : 83.33 % 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: 4.99 (0.39), residues: 476 helix: 3.74 (0.25), residues: 400 sheet: None (None), residues: 0 loop : 0.50 (0.84), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 184 HIS 0.002 0.001 HIS B 72 PHE 0.011 0.001 PHE B 246 TYR 0.017 0.002 TYR B 85 ARG 0.003 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8038 (tp30) cc_final: 0.7701 (tp30) REVERT: A 135 PHE cc_start: 0.7330 (t80) cc_final: 0.6135 (m-10) REVERT: B 135 PHE cc_start: 0.7298 (t80) cc_final: 0.6165 (m-10) REVERT: B 168 MET cc_start: 0.8145 (mmm) cc_final: 0.7714 (mmt) outliers start: 9 outliers final: 4 residues processed: 91 average time/residue: 0.2306 time to fit residues: 24.8334 Evaluate side-chains 81 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 139 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 46 optimal weight: 0.0770 chunk 41 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4156 Z= 0.181 Angle : 0.519 7.111 5644 Z= 0.270 Chirality : 0.036 0.161 650 Planarity : 0.003 0.017 664 Dihedral : 4.712 35.523 952 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.21 % Allowed : 15.20 % Favored : 82.60 % 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: 4.88 (0.39), residues: 476 helix: 3.68 (0.25), residues: 400 sheet: None (None), residues: 0 loop : 0.30 (0.84), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 184 HIS 0.001 0.000 HIS B 72 PHE 0.009 0.001 PHE B 246 TYR 0.013 0.001 TYR B 85 ARG 0.003 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.7463 (pt0) cc_final: 0.7216 (pt0) REVERT: A 135 PHE cc_start: 0.7358 (t80) cc_final: 0.6157 (m-10) REVERT: A 168 MET cc_start: 0.8145 (mmm) cc_final: 0.7751 (mmt) REVERT: B 70 GLU cc_start: 0.7522 (pt0) cc_final: 0.7306 (pt0) REVERT: B 135 PHE cc_start: 0.7343 (t80) cc_final: 0.6204 (m-10) REVERT: B 168 MET cc_start: 0.8148 (mmm) cc_final: 0.7776 (mmt) outliers start: 9 outliers final: 8 residues processed: 88 average time/residue: 0.2191 time to fit residues: 22.6407 Evaluate side-chains 84 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 139 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.0980 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4156 Z= 0.209 Angle : 0.539 7.700 5644 Z= 0.281 Chirality : 0.036 0.154 650 Planarity : 0.003 0.018 664 Dihedral : 4.629 34.522 952 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.45 % Allowed : 15.44 % Favored : 82.11 % 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: 4.84 (0.39), residues: 476 helix: 3.67 (0.25), residues: 398 sheet: None (None), residues: 0 loop : 0.32 (0.82), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 184 HIS 0.001 0.000 HIS B 72 PHE 0.009 0.001 PHE B 223 TYR 0.014 0.001 TYR B 85 ARG 0.002 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8123 (tt) REVERT: A 38 GLU cc_start: 0.8111 (tp30) cc_final: 0.7784 (tp30) REVERT: A 135 PHE cc_start: 0.7338 (t80) cc_final: 0.6138 (m-10) REVERT: A 168 MET cc_start: 0.8104 (mmm) cc_final: 0.7648 (mmm) REVERT: B 29 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8122 (tt) REVERT: B 135 PHE cc_start: 0.7360 (t80) cc_final: 0.6195 (m-10) REVERT: B 168 MET cc_start: 0.8170 (mmm) cc_final: 0.7672 (mmm) REVERT: B 227 TYR cc_start: 0.8666 (t80) cc_final: 0.8206 (t80) outliers start: 10 outliers final: 7 residues processed: 88 average time/residue: 0.2261 time to fit residues: 23.3749 Evaluate side-chains 90 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 139 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.0870 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 GLN B 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4156 Z= 0.243 Angle : 0.570 9.626 5644 Z= 0.294 Chirality : 0.037 0.164 650 Planarity : 0.003 0.017 664 Dihedral : 4.723 39.409 952 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.70 % Allowed : 17.16 % Favored : 80.15 % 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 (0.39), residues: 476 helix: 3.54 (0.25), residues: 400 sheet: None (None), residues: 0 loop : -0.16 (0.80), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 184 HIS 0.001 0.000 HIS B 188 PHE 0.010 0.001 PHE A 16 TYR 0.018 0.002 TYR B 85 ARG 0.002 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8159 (tt) REVERT: A 70 GLU cc_start: 0.7514 (pt0) cc_final: 0.7086 (pm20) REVERT: A 168 MET cc_start: 0.8153 (mmm) cc_final: 0.7750 (mmm) REVERT: B 29 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8195 (tt) REVERT: B 38 GLU cc_start: 0.8093 (tp30) cc_final: 0.7803 (tp30) REVERT: B 66 ILE cc_start: 0.7830 (mt) cc_final: 0.7294 (mm) REVERT: B 70 GLU cc_start: 0.7619 (pt0) cc_final: 0.7084 (pm20) outliers start: 11 outliers final: 8 residues processed: 89 average time/residue: 0.2178 time to fit residues: 22.8616 Evaluate side-chains 93 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 139 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4156 Z= 0.197 Angle : 0.545 6.832 5644 Z= 0.285 Chirality : 0.035 0.150 650 Planarity : 0.002 0.016 664 Dihedral : 4.664 39.699 952 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.94 % Allowed : 18.87 % Favored : 78.19 % 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: 4.73 (0.39), residues: 476 helix: 3.65 (0.25), residues: 400 sheet: None (None), residues: 0 loop : -0.15 (0.81), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 184 HIS 0.000 0.000 HIS A 72 PHE 0.029 0.001 PHE B 112 TYR 0.013 0.001 TYR B 113 ARG 0.002 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8143 (tt) REVERT: A 38 GLU cc_start: 0.8095 (tp30) cc_final: 0.7815 (tp30) REVERT: A 135 PHE cc_start: 0.6980 (t80) cc_final: 0.5860 (m-10) REVERT: A 168 MET cc_start: 0.8123 (mmm) cc_final: 0.7747 (mmm) REVERT: B 29 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8178 (tt) REVERT: B 135 PHE cc_start: 0.7039 (t80) cc_final: 0.5906 (m-10) outliers start: 12 outliers final: 7 residues processed: 87 average time/residue: 0.2290 time to fit residues: 23.4144 Evaluate side-chains 94 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4156 Z= 0.223 Angle : 0.582 9.330 5644 Z= 0.302 Chirality : 0.037 0.154 650 Planarity : 0.002 0.017 664 Dihedral : 4.689 40.375 952 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.43 % Allowed : 18.63 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.69 (0.39), residues: 476 helix: 3.63 (0.25), residues: 400 sheet: None (None), residues: 0 loop : -0.23 (0.82), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 184 HIS 0.000 0.000 HIS A 98 PHE 0.026 0.001 PHE B 112 TYR 0.013 0.001 TYR B 85 ARG 0.002 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8156 (tt) REVERT: A 38 GLU cc_start: 0.8138 (tp30) cc_final: 0.7876 (tp30) REVERT: A 135 PHE cc_start: 0.6886 (t80) cc_final: 0.5788 (m-10) REVERT: A 168 MET cc_start: 0.8130 (mmm) cc_final: 0.7727 (mmm) REVERT: A 227 TYR cc_start: 0.8750 (t80) cc_final: 0.8208 (t80) REVERT: B 29 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8182 (tt) REVERT: B 135 PHE cc_start: 0.6919 (t80) cc_final: 0.5843 (m-10) REVERT: B 227 TYR cc_start: 0.8754 (t80) cc_final: 0.8208 (t80) outliers start: 14 outliers final: 7 residues processed: 94 average time/residue: 0.2204 time to fit residues: 24.3279 Evaluate side-chains 91 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8000 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4156 Z= 0.231 Angle : 0.595 9.864 5644 Z= 0.312 Chirality : 0.037 0.167 650 Planarity : 0.002 0.015 664 Dihedral : 4.728 41.776 952 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.19 % Allowed : 18.38 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.66 (0.39), residues: 476 helix: 3.60 (0.25), residues: 400 sheet: None (None), residues: 0 loop : -0.20 (0.82), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 184 HIS 0.001 0.000 HIS A 188 PHE 0.027 0.001 PHE B 112 TYR 0.013 0.002 TYR B 85 ARG 0.001 0.000 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8158 (tt) REVERT: A 38 GLU cc_start: 0.8168 (tp30) cc_final: 0.7881 (tp30) REVERT: A 135 PHE cc_start: 0.6880 (t80) cc_final: 0.5791 (m-10) REVERT: A 168 MET cc_start: 0.8158 (mmm) cc_final: 0.7793 (mmm) REVERT: A 227 TYR cc_start: 0.8774 (t80) cc_final: 0.8218 (t80) REVERT: B 29 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8194 (tt) REVERT: B 38 GLU cc_start: 0.8141 (tp30) cc_final: 0.7863 (tp30) REVERT: B 70 GLU cc_start: 0.7515 (pt0) cc_final: 0.6857 (pm20) REVERT: B 135 PHE cc_start: 0.6936 (t80) cc_final: 0.5874 (m-10) REVERT: B 227 TYR cc_start: 0.8786 (t80) cc_final: 0.8223 (t80) outliers start: 13 outliers final: 9 residues processed: 94 average time/residue: 0.2240 time to fit residues: 24.9850 Evaluate side-chains 94 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.8043 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4156 Z= 0.305 Angle : 0.644 10.113 5644 Z= 0.339 Chirality : 0.039 0.165 650 Planarity : 0.003 0.016 664 Dihedral : 4.939 42.406 952 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.68 % Allowed : 18.38 % Favored : 77.94 % 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: 4.41 (0.39), residues: 476 helix: 3.43 (0.25), residues: 400 sheet: None (None), residues: 0 loop : -0.31 (0.83), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 184 HIS 0.001 0.000 HIS A 98 PHE 0.028 0.002 PHE B 112 TYR 0.015 0.002 TYR A 85 ARG 0.002 0.000 ARG A 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8209 (tt) REVERT: A 38 GLU cc_start: 0.8172 (tp30) cc_final: 0.7888 (tp30) REVERT: A 168 MET cc_start: 0.8201 (mmm) cc_final: 0.7888 (mmm) REVERT: B 29 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8247 (tt) REVERT: B 70 GLU cc_start: 0.7679 (pt0) cc_final: 0.7091 (pm20) outliers start: 15 outliers final: 11 residues processed: 91 average time/residue: 0.2280 time to fit residues: 24.3135 Evaluate side-chains 98 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.181033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.134808 restraints weight = 4230.795| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.16 r_work: 0.3060 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4156 Z= 0.255 Angle : 0.605 7.324 5644 Z= 0.317 Chirality : 0.037 0.159 650 Planarity : 0.003 0.019 664 Dihedral : 4.970 44.786 952 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.19 % Allowed : 18.38 % Favored : 78.43 % 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: 4.42 (0.39), residues: 476 helix: 3.44 (0.25), residues: 400 sheet: None (None), residues: 0 loop : -0.34 (0.81), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 184 HIS 0.001 0.000 HIS B 188 PHE 0.026 0.001 PHE B 112 TYR 0.020 0.002 TYR B 59 ARG 0.005 0.000 ARG B 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1173.01 seconds wall clock time: 21 minutes 38.25 seconds (1298.25 seconds total)