Starting phenix.real_space_refine on Thu Nov 14 04:02:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g2w_50986/11_2024/9g2w_50986.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g2w_50986/11_2024/9g2w_50986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g2w_50986/11_2024/9g2w_50986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g2w_50986/11_2024/9g2w_50986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g2w_50986/11_2024/9g2w_50986.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g2w_50986/11_2024/9g2w_50986.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2404 2.51 5 N 677 2.21 5 O 741 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3838 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1939 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain: "B" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1899 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 1 Time building chain proxies: 3.10, per 1000 atoms: 0.81 Number of scatterers: 3838 At special positions: 0 Unit cell: (114.208, 83.664, 115.536, 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 16 16.00 O 741 8.00 N 677 7.00 C 2404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 467.5 milliseconds 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 914 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 93.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 11 through 30 removed outlier: 3.654A pdb=" N ALA A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 68 Processing helix chain 'A' and resid 70 through 84 removed outlier: 3.578A pdb=" N ARG A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 109 Processing helix chain 'A' and resid 112 through 143 Processing helix chain 'A' and resid 143 through 181 removed outlier: 4.107A pdb=" N TYR A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 215 removed outlier: 3.972A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 252 removed outlier: 3.884A pdb=" N THR A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 30 Processing helix chain 'B' and resid 39 through 68 Processing helix chain 'B' and resid 70 through 84 removed outlier: 3.520A pdb=" N ARG B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 109 Processing helix chain 'B' and resid 112 through 143 Processing helix chain 'B' and resid 143 through 153 removed outlier: 3.529A pdb=" N LEU B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 181 removed outlier: 3.541A pdb=" N THR B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 215 Processing helix chain 'B' and resid 215 through 252 367 hydrogen bonds defined for protein. 1101 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: 1.04 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 859 1.33 - 1.45: 760 1.45 - 1.57: 2248 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3891 Sorted by residual: bond pdb=" N ILE A 91 " pdb=" CA ILE A 91 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.20e-02 6.94e+03 8.44e+00 bond pdb=" N ILE A 216 " pdb=" CA ILE A 216 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.26e-02 6.30e+03 7.96e+00 bond pdb=" N ASN A 93 " pdb=" CA ASN A 93 " ideal model delta sigma weight residual 1.462 1.488 -0.026 9.50e-03 1.11e+04 7.61e+00 bond pdb=" N ILE A 75 " pdb=" CA ILE A 75 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.59e+00 bond pdb=" N ILE B 151 " pdb=" CA ILE B 151 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.26e-02 6.30e+03 7.58e+00 ... (remaining 3886 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 3763 1.04 - 2.09: 775 2.09 - 3.13: 652 3.13 - 4.18: 36 4.18 - 5.22: 9 Bond angle restraints: 5235 Sorted by residual: angle pdb=" N LEU A 30 " pdb=" CA LEU A 30 " pdb=" C LEU A 30 " ideal model delta sigma weight residual 112.87 108.08 4.79 1.20e+00 6.94e-01 1.59e+01 angle pdb=" N GLY A 31 " pdb=" CA GLY A 31 " pdb=" C GLY A 31 " ideal model delta sigma weight residual 115.40 110.27 5.13 1.32e+00 5.74e-01 1.51e+01 angle pdb=" N GLU B 214 " pdb=" CA GLU B 214 " pdb=" C GLU B 214 " ideal model delta sigma weight residual 113.23 108.50 4.73 1.24e+00 6.50e-01 1.45e+01 angle pdb=" CA ALA B 182 " pdb=" C ALA B 182 " pdb=" O ALA B 182 " ideal model delta sigma weight residual 122.64 118.13 4.51 1.25e+00 6.40e-01 1.30e+01 angle pdb=" N LEU A 83 " pdb=" CA LEU A 83 " pdb=" C LEU A 83 " ideal model delta sigma weight residual 113.01 108.81 4.20 1.20e+00 6.94e-01 1.23e+01 ... (remaining 5230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.50: 2167 15.50 - 31.00: 169 31.00 - 46.50: 47 46.50 - 62.00: 30 62.00 - 77.50: 6 Dihedral angle restraints: 2419 sinusoidal: 1014 harmonic: 1405 Sorted by residual: dihedral pdb=" CD ARG B 210 " pdb=" NE ARG B 210 " pdb=" CZ ARG B 210 " pdb=" NH1 ARG B 210 " ideal model delta sinusoidal sigma weight residual 0.00 32.61 -32.61 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" CD ARG B 169 " pdb=" NE ARG B 169 " pdb=" CZ ARG B 169 " pdb=" NH1 ARG B 169 " ideal model delta sinusoidal sigma weight residual 0.00 -27.47 27.47 1 1.00e+01 1.00e-02 1.08e+01 dihedral pdb=" CD ARG B 225 " pdb=" NE ARG B 225 " pdb=" CZ ARG B 225 " pdb=" NH1 ARG B 225 " ideal model delta sinusoidal sigma weight residual 0.00 -26.98 26.98 1 1.00e+01 1.00e-02 1.05e+01 ... (remaining 2416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 271 0.043 - 0.085: 105 0.085 - 0.127: 124 0.127 - 0.169: 62 0.169 - 0.211: 28 Chirality restraints: 590 Sorted by residual: chirality pdb=" CA ILE A 208 " pdb=" N ILE A 208 " pdb=" C ILE A 208 " pdb=" CB ILE A 208 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ASP B 203 " pdb=" N ASP B 203 " pdb=" C ASP B 203 " pdb=" CB ASP B 203 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE A 75 " pdb=" N ILE A 75 " pdb=" C ILE A 75 " pdb=" CB ILE A 75 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 587 not shown) Planarity restraints: 681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 210 " -0.574 9.50e-02 1.11e+02 2.57e-01 4.04e+01 pdb=" NE ARG B 210 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG B 210 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 210 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 210 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 169 " -0.493 9.50e-02 1.11e+02 2.21e-01 2.99e+01 pdb=" NE ARG B 169 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG B 169 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 169 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 169 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 225 " 0.487 9.50e-02 1.11e+02 2.18e-01 2.92e+01 pdb=" NE ARG B 225 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 225 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 225 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 225 " 0.016 2.00e-02 2.50e+03 ... (remaining 678 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1456 2.86 - 3.37: 4479 3.37 - 3.88: 6652 3.88 - 4.39: 7661 4.39 - 4.90: 11287 Nonbonded interactions: 31535 Sorted by model distance: nonbonded pdb=" O SER B 200 " pdb=" OD1 ASP B 203 " model vdw 2.354 3.040 nonbonded pdb=" O LEU B 195 " pdb=" OG1 THR B 198 " model vdw 2.399 3.040 nonbonded pdb=" NE2 GLN A 243 " pdb=" OD1 ASP A 247 " model vdw 2.399 3.120 nonbonded pdb=" O ASP A 14 " pdb=" OG1 THR A 17 " model vdw 2.414 3.040 nonbonded pdb=" N GLU A 186 " pdb=" OE1 GLU A 186 " model vdw 2.419 3.120 ... (remaining 31530 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 30 or resid 35 through 252)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.800 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 : 0.009 0.044 3891 Z= 0.567 Angle : 1.167 5.221 5235 Z= 0.968 Chirality : 0.084 0.211 590 Planarity : 0.024 0.257 681 Dihedral : 14.466 77.496 1505 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.73 % Allowed : 5.11 % Favored : 94.16 % 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: -0.44 (0.34), residues: 472 helix: -0.00 (0.22), residues: 430 sheet: None (None), residues: 0 loop : -1.86 (0.79), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 55 HIS 0.007 0.002 HIS B 41 PHE 0.028 0.002 PHE B 78 TYR 0.023 0.002 TYR A 244 ARG 0.036 0.004 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8484 (tm-30) REVERT: B 235 MET cc_start: 0.8855 (tmm) cc_final: 0.8616 (tmm) outliers start: 3 outliers final: 0 residues processed: 78 average time/residue: 0.1676 time to fit residues: 16.1507 Evaluate side-chains 43 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN B 228 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3891 Z= 0.179 Angle : 0.534 9.727 5235 Z= 0.289 Chirality : 0.033 0.122 590 Planarity : 0.004 0.032 681 Dihedral : 3.015 12.251 521 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.46 % Allowed : 9.49 % Favored : 89.05 % 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: 4.80 (0.35), residues: 472 helix: 3.38 (0.22), residues: 435 sheet: None (None), residues: 0 loop : -0.24 (0.89), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 55 HIS 0.007 0.001 HIS A 41 PHE 0.021 0.002 PHE B 78 TYR 0.019 0.001 TYR A 244 ARG 0.006 0.001 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7489 (mt-10) REVERT: A 121 CYS cc_start: 0.8401 (t) cc_final: 0.8054 (t) REVERT: B 64 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8482 (tm-30) REVERT: B 125 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8579 (mp10) REVERT: B 235 MET cc_start: 0.8986 (tmm) cc_final: 0.8619 (tmm) REVERT: B 245 MET cc_start: 0.9277 (tpp) cc_final: 0.8975 (tpp) outliers start: 6 outliers final: 3 residues processed: 55 average time/residue: 0.1653 time to fit residues: 11.4891 Evaluate side-chains 44 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 234 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3891 Z= 0.165 Angle : 0.547 9.800 5235 Z= 0.278 Chirality : 0.033 0.116 590 Planarity : 0.004 0.035 681 Dihedral : 2.978 12.454 521 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.70 % Allowed : 10.22 % Favored : 88.08 % 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: 6.03 (0.35), residues: 472 helix: 4.18 (0.22), residues: 434 sheet: None (None), residues: 0 loop : 0.24 (0.92), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 55 HIS 0.008 0.001 HIS A 41 PHE 0.025 0.002 PHE A 25 TYR 0.020 0.001 TYR A 244 ARG 0.006 0.001 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 CYS cc_start: 0.8352 (t) cc_final: 0.7950 (t) REVERT: A 179 LEU cc_start: 0.9381 (tt) cc_final: 0.9055 (pp) REVERT: B 103 ASP cc_start: 0.8701 (t0) cc_final: 0.8193 (t0) REVERT: B 125 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8679 (mp10) REVERT: B 235 MET cc_start: 0.8951 (tmm) cc_final: 0.8677 (tmm) REVERT: B 245 MET cc_start: 0.9231 (tpp) cc_final: 0.8904 (tpp) outliers start: 7 outliers final: 4 residues processed: 48 average time/residue: 0.1546 time to fit residues: 9.6877 Evaluate side-chains 43 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3891 Z= 0.165 Angle : 0.508 7.341 5235 Z= 0.268 Chirality : 0.032 0.115 590 Planarity : 0.003 0.031 681 Dihedral : 3.000 12.399 521 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.70 % Allowed : 11.44 % Favored : 86.86 % 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: 6.12 (0.35), residues: 472 helix: 4.24 (0.22), residues: 435 sheet: None (None), residues: 0 loop : 0.10 (0.91), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 55 HIS 0.007 0.001 HIS A 41 PHE 0.009 0.001 PHE A 150 TYR 0.012 0.001 TYR B 242 ARG 0.003 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 CYS cc_start: 0.8525 (t) cc_final: 0.8080 (t) REVERT: B 125 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8582 (mp10) REVERT: B 235 MET cc_start: 0.8909 (tmm) cc_final: 0.8643 (tmm) REVERT: B 245 MET cc_start: 0.9213 (tpp) cc_final: 0.8905 (tpp) outliers start: 7 outliers final: 4 residues processed: 44 average time/residue: 0.1512 time to fit residues: 8.8666 Evaluate side-chains 39 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3891 Z= 0.177 Angle : 0.508 6.986 5235 Z= 0.266 Chirality : 0.032 0.122 590 Planarity : 0.003 0.030 681 Dihedral : 3.087 15.607 521 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.19 % Allowed : 10.71 % Favored : 87.10 % 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: 6.15 (0.35), residues: 472 helix: 4.25 (0.22), residues: 435 sheet: None (None), residues: 0 loop : 0.26 (0.93), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 55 HIS 0.006 0.001 HIS A 41 PHE 0.025 0.002 PHE A 78 TYR 0.024 0.001 TYR B 242 ARG 0.005 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 CYS cc_start: 0.8603 (t) cc_final: 0.8132 (t) REVERT: A 235 MET cc_start: 0.9008 (tpp) cc_final: 0.8537 (tmm) REVERT: B 103 ASP cc_start: 0.8737 (t0) cc_final: 0.8141 (t0) REVERT: B 125 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8606 (mp10) REVERT: B 235 MET cc_start: 0.8885 (tmm) cc_final: 0.8596 (tmm) REVERT: B 245 MET cc_start: 0.9207 (tpp) cc_final: 0.8811 (tpp) outliers start: 9 outliers final: 6 residues processed: 42 average time/residue: 0.1552 time to fit residues: 8.5661 Evaluate side-chains 42 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3891 Z= 0.153 Angle : 0.497 7.705 5235 Z= 0.261 Chirality : 0.032 0.119 590 Planarity : 0.003 0.029 681 Dihedral : 3.097 16.416 521 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.19 % Allowed : 10.95 % Favored : 86.86 % 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: 6.20 (0.35), residues: 472 helix: 4.28 (0.22), residues: 435 sheet: None (None), residues: 0 loop : 0.30 (0.93), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 55 HIS 0.008 0.001 HIS A 41 PHE 0.016 0.001 PHE A 25 TYR 0.020 0.001 TYR B 242 ARG 0.002 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 CYS cc_start: 0.8548 (t) cc_final: 0.8096 (t) REVERT: A 235 MET cc_start: 0.9018 (tpp) cc_final: 0.8447 (tmm) REVERT: B 125 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8630 (mp10) REVERT: B 245 MET cc_start: 0.9192 (tpp) cc_final: 0.8797 (tpp) outliers start: 9 outliers final: 4 residues processed: 45 average time/residue: 0.2069 time to fit residues: 12.1348 Evaluate side-chains 40 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 165 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 45 optimal weight: 0.0980 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3891 Z= 0.143 Angle : 0.518 7.153 5235 Z= 0.264 Chirality : 0.033 0.174 590 Planarity : 0.003 0.028 681 Dihedral : 3.091 17.068 521 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.22 % Allowed : 12.41 % Favored : 86.37 % 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: 6.32 (0.35), residues: 472 helix: 4.36 (0.22), residues: 434 sheet: None (None), residues: 0 loop : 0.41 (0.92), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 55 HIS 0.005 0.001 HIS A 41 PHE 0.027 0.002 PHE A 78 TYR 0.021 0.002 TYR A 244 ARG 0.002 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 CYS cc_start: 0.8338 (t) cc_final: 0.7926 (t) REVERT: A 235 MET cc_start: 0.9005 (tpp) cc_final: 0.8460 (tmm) REVERT: B 103 ASP cc_start: 0.8793 (t0) cc_final: 0.8130 (t0) REVERT: B 125 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8625 (mp10) REVERT: B 245 MET cc_start: 0.9196 (tpp) cc_final: 0.8861 (tpp) REVERT: B 248 LEU cc_start: 0.8619 (tt) cc_final: 0.8356 (tt) outliers start: 5 outliers final: 3 residues processed: 46 average time/residue: 0.1521 time to fit residues: 9.1264 Evaluate side-chains 44 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 43 optimal weight: 0.0670 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3891 Z= 0.159 Angle : 0.530 6.848 5235 Z= 0.275 Chirality : 0.033 0.147 590 Planarity : 0.003 0.027 681 Dihedral : 3.117 17.532 521 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.46 % Allowed : 13.63 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.24 (0.35), residues: 472 helix: 4.30 (0.22), residues: 435 sheet: None (None), residues: 0 loop : 0.32 (0.93), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 55 HIS 0.004 0.001 HIS B 41 PHE 0.026 0.002 PHE A 78 TYR 0.028 0.002 TYR A 244 ARG 0.003 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 CYS cc_start: 0.8332 (t) cc_final: 0.8126 (t) REVERT: A 235 MET cc_start: 0.8993 (tpp) cc_final: 0.8444 (tmm) REVERT: B 103 ASP cc_start: 0.8840 (t0) cc_final: 0.8290 (t0) REVERT: B 125 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8623 (mp10) REVERT: B 245 MET cc_start: 0.9217 (tpp) cc_final: 0.8795 (tpp) outliers start: 6 outliers final: 4 residues processed: 45 average time/residue: 0.1573 time to fit residues: 9.4332 Evaluate side-chains 41 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.0170 chunk 46 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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: 0.8224 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3891 Z= 0.149 Angle : 0.558 7.718 5235 Z= 0.286 Chirality : 0.033 0.174 590 Planarity : 0.003 0.027 681 Dihedral : 3.134 17.602 521 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 0.97 % Allowed : 14.60 % Favored : 84.43 % 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: 6.19 (0.35), residues: 472 helix: 4.28 (0.22), residues: 434 sheet: None (None), residues: 0 loop : 0.33 (0.92), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 55 HIS 0.005 0.001 HIS B 41 PHE 0.027 0.002 PHE A 78 TYR 0.035 0.002 TYR A 244 ARG 0.003 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.8995 (tpp) cc_final: 0.8430 (tmm) REVERT: B 103 ASP cc_start: 0.8834 (t0) cc_final: 0.8271 (t0) REVERT: B 125 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8604 (mp10) REVERT: B 245 MET cc_start: 0.9222 (tpp) cc_final: 0.8819 (tpp) outliers start: 4 outliers final: 3 residues processed: 42 average time/residue: 0.1531 time to fit residues: 8.5875 Evaluate side-chains 42 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS B 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3891 Z= 0.156 Angle : 0.567 7.316 5235 Z= 0.290 Chirality : 0.033 0.163 590 Planarity : 0.003 0.026 681 Dihedral : 3.154 17.609 521 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.46 % Allowed : 14.60 % Favored : 83.94 % 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: 6.04 (0.35), residues: 472 helix: 4.18 (0.22), residues: 434 sheet: None (None), residues: 0 loop : 0.37 (0.92), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 55 HIS 0.005 0.001 HIS B 41 PHE 0.027 0.002 PHE A 78 TYR 0.018 0.002 TYR A 155 ARG 0.003 0.000 ARG A 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.8969 (tpp) cc_final: 0.8396 (tmm) REVERT: B 125 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8646 (mp10) REVERT: B 235 MET cc_start: 0.8773 (tmm) cc_final: 0.8439 (tmm) REVERT: B 245 MET cc_start: 0.9211 (tpp) cc_final: 0.8790 (tpp) outliers start: 6 outliers final: 4 residues processed: 42 average time/residue: 0.1436 time to fit residues: 8.0798 Evaluate side-chains 42 residues out of total 411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 2 optimal weight: 0.0020 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 0.0170 chunk 1 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.5430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.061936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.048463 restraints weight = 19658.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.050052 restraints weight = 9497.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.051121 restraints weight = 5857.446| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3891 Z= 0.154 Angle : 0.569 7.172 5235 Z= 0.292 Chirality : 0.034 0.178 590 Planarity : 0.003 0.026 681 Dihedral : 3.140 17.666 521 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.22 % Allowed : 15.09 % Favored : 83.70 % 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: 6.05 (0.35), residues: 472 helix: 4.18 (0.22), residues: 434 sheet: None (None), residues: 0 loop : 0.39 (0.92), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 55 HIS 0.013 0.002 HIS B 41 PHE 0.027 0.002 PHE A 78 TYR 0.018 0.002 TYR A 155 ARG 0.002 0.000 ARG A 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1045.52 seconds wall clock time: 19 minutes 51.08 seconds (1191.08 seconds total)