Starting phenix.real_space_refine on Thu Jul 18 20:59:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc6_40339/07_2024/8sc6_40339.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc6_40339/07_2024/8sc6_40339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc6_40339/07_2024/8sc6_40339.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc6_40339/07_2024/8sc6_40339.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc6_40339/07_2024/8sc6_40339.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sc6_40339/07_2024/8sc6_40339.cif" } resolution = 3.13 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= 0.034 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 31 5.16 5 C 2293 2.51 5 N 565 2.21 5 O 590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 3479 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3461 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 1 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'VIB': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.01, per 1000 atoms: 0.87 Number of scatterers: 3479 At special positions: 0 Unit cell: (90.72, 84, 68.04, 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 31 16.00 O 590 8.00 N 565 7.00 C 2293 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.03 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: 1.45 Conformation dependent library (CDL) restraints added in 549.6 milliseconds 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 818 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 80.5% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.959A pdb=" N LEU A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 removed outlier: 3.727A pdb=" N CYS A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 141 through 147 removed outlier: 4.520A pdb=" N TRP A 146 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 173 removed outlier: 4.333A pdb=" N GLN A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 194 removed outlier: 3.820A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 removed outlier: 3.738A pdb=" N VAL A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 258 removed outlier: 3.612A pdb=" N GLN A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 278 Proline residue: A 271 - end of helix removed outlier: 3.515A pdb=" N LEU A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 339 removed outlier: 3.504A pdb=" N PHE A 338 " --> pdb=" O ALA A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 372 Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.508A pdb=" N VAL A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 398 removed outlier: 4.072A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 420 removed outlier: 3.542A pdb=" N MET A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 removed outlier: 3.738A pdb=" N ILE A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 491 removed outlier: 3.788A pdb=" N LEU A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) Proline residue: A 481 - end of helix removed outlier: 3.533A pdb=" N LEU A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 removed outlier: 4.019A pdb=" N LEU A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 241 hydrogen bonds defined for protein. 696 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: 0.92 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1071 1.34 - 1.46: 838 1.46 - 1.58: 1616 1.58 - 1.69: 1 1.69 - 1.81: 46 Bond restraints: 3572 Sorted by residual: bond pdb=" CA LEU A 427 " pdb=" C LEU A 427 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.14e-02 7.69e+03 5.00e-01 bond pdb=" N VAL A 74 " pdb=" CA VAL A 74 " ideal model delta sigma weight residual 1.468 1.461 0.007 1.05e-02 9.07e+03 4.84e-01 bond pdb=" CA THR A 480 " pdb=" C THR A 480 " ideal model delta sigma weight residual 1.520 1.529 -0.008 1.23e-02 6.61e+03 4.75e-01 bond pdb=" C ALA A 257 " pdb=" N LEU A 258 " ideal model delta sigma weight residual 1.327 1.336 -0.009 1.32e-02 5.74e+03 4.45e-01 bond pdb=" C VAL A 461 " pdb=" O VAL A 461 " ideal model delta sigma weight residual 1.226 1.240 -0.013 2.04e-02 2.40e+03 4.30e-01 ... (remaining 3567 not shown) Histogram of bond angle deviations from ideal: 91.52 - 100.01: 1 100.01 - 108.49: 162 108.49 - 116.98: 2236 116.98 - 125.47: 2396 125.47 - 133.95: 75 Bond angle restraints: 4870 Sorted by residual: angle pdb=" C GLU A 386 " pdb=" N ILE A 387 " pdb=" CA ILE A 387 " ideal model delta sigma weight residual 120.33 122.81 -2.48 8.00e-01 1.56e+00 9.59e+00 angle pdb=" C TYR A 72 " pdb=" N THR A 73 " pdb=" CA THR A 73 " ideal model delta sigma weight residual 122.46 117.60 4.86 1.80e+00 3.09e-01 7.30e+00 angle pdb=" CA CYS A 50 " pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " ideal model delta sigma weight residual 114.40 119.23 -4.83 2.30e+00 1.89e-01 4.40e+00 angle pdb=" N THR A 480 " pdb=" CA THR A 480 " pdb=" C THR A 480 " ideal model delta sigma weight residual 112.75 115.58 -2.83 1.36e+00 5.41e-01 4.34e+00 angle pdb=" C VAL A 461 " pdb=" CA VAL A 461 " pdb=" CB VAL A 461 " ideal model delta sigma weight residual 112.36 109.75 2.61 1.37e+00 5.33e-01 3.62e+00 ... (remaining 4865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.01: 1882 11.01 - 22.02: 141 22.02 - 33.03: 34 33.03 - 44.04: 9 44.04 - 55.05: 1 Dihedral angle restraints: 2067 sinusoidal: 788 harmonic: 1279 Sorted by residual: dihedral pdb=" N PHE A 273 " pdb=" CA PHE A 273 " pdb=" CB PHE A 273 " pdb=" CG PHE A 273 " ideal model delta sinusoidal sigma weight residual -60.00 -115.05 55.05 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" N LEU A 150 " pdb=" CA LEU A 150 " pdb=" CB LEU A 150 " pdb=" CG LEU A 150 " ideal model delta sinusoidal sigma weight residual -60.00 -102.93 42.93 3 1.50e+01 4.44e-03 7.71e+00 dihedral pdb=" N MET A 239 " pdb=" CA MET A 239 " pdb=" CB MET A 239 " pdb=" CG MET A 239 " ideal model delta sinusoidal sigma weight residual -180.00 -141.24 -38.76 3 1.50e+01 4.44e-03 6.84e+00 ... (remaining 2064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 313 0.022 - 0.043: 148 0.043 - 0.065: 63 0.065 - 0.087: 18 0.087 - 0.109: 20 Chirality restraints: 562 Sorted by residual: chirality pdb=" CA THR A 480 " pdb=" N THR A 480 " pdb=" C THR A 480 " pdb=" CB THR A 480 " both_signs ideal model delta sigma weight residual False 2.53 2.42 0.11 2.00e-01 2.50e+01 2.95e-01 chirality pdb=" CA LEU A 270 " pdb=" N LEU A 270 " pdb=" C LEU A 270 " pdb=" CB LEU A 270 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.88e-01 chirality pdb=" CA PRO A 53 " pdb=" N PRO A 53 " pdb=" C PRO A 53 " pdb=" CB PRO A 53 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.84e-01 ... (remaining 559 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.52e+00 pdb=" N PRO A 271 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 74 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO A 75 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 65 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 66 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.016 5.00e-02 4.00e+02 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 868 2.80 - 3.32: 3411 3.32 - 3.85: 5504 3.85 - 4.37: 6251 4.37 - 4.90: 11184 Nonbonded interactions: 27218 Sorted by model distance: nonbonded pdb=" O LYS A 147 " pdb=" OH TYR A 199 " model vdw 2.273 2.440 nonbonded pdb=" OE1 GLU A 137 " pdb=" NE1 TRP A 261 " model vdw 2.340 2.520 nonbonded pdb=" NZ LYS A 214 " pdb=" OD1 ASP A 474 " model vdw 2.351 2.520 nonbonded pdb=" O GLY A 476 " pdb=" OG1 THR A 480 " model vdw 2.353 2.440 nonbonded pdb=" O GLN A 209 " pdb=" OG SER A 213 " model vdw 2.363 2.440 ... (remaining 27213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.820 Find NCS groups from input model: 0.040 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 : 0.003 0.023 3572 Z= 0.166 Angle : 0.502 5.291 4870 Z= 0.288 Chirality : 0.035 0.109 562 Planarity : 0.004 0.031 601 Dihedral : 8.707 55.052 1240 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.81 % Allowed : 2.96 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.41), residues: 443 helix: 2.09 (0.31), residues: 302 sheet: None (None), residues: 0 loop : 1.57 (0.57), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 244 TYR 0.011 0.001 TYR A 168 ARG 0.001 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.377 Fit side-chains REVERT: A 273 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: A 351 MET cc_start: 0.8709 (mtt) cc_final: 0.8385 (mtp) REVERT: A 357 ASP cc_start: 0.7980 (m-30) cc_final: 0.7731 (m-30) outliers start: 3 outliers final: 0 residues processed: 67 average time/residue: 0.1692 time to fit residues: 13.7407 Evaluate side-chains 41 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 115 HIS A 447 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3572 Z= 0.225 Angle : 0.501 6.685 4870 Z= 0.258 Chirality : 0.037 0.132 562 Planarity : 0.004 0.033 601 Dihedral : 4.747 54.075 487 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.43 % Allowed : 9.97 % Favored : 87.60 % 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: 2.89 (0.41), residues: 443 helix: 2.27 (0.30), residues: 305 sheet: None (None), residues: 0 loop : 1.30 (0.58), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.004 0.001 HIS A 49 PHE 0.011 0.001 PHE A 32 TYR 0.012 0.001 TYR A 168 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.327 Fit side-chains REVERT: A 273 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7764 (m-80) REVERT: A 351 MET cc_start: 0.8692 (mtt) cc_final: 0.8463 (mtm) REVERT: A 357 ASP cc_start: 0.8031 (m-30) cc_final: 0.7810 (m-30) outliers start: 9 outliers final: 5 residues processed: 51 average time/residue: 0.1408 time to fit residues: 9.1873 Evaluate side-chains 47 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 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 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3572 Z= 0.176 Angle : 0.450 4.950 4870 Z= 0.232 Chirality : 0.036 0.124 562 Planarity : 0.004 0.030 601 Dihedral : 4.645 55.204 487 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.16 % Allowed : 9.70 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.41), residues: 443 helix: 2.37 (0.30), residues: 306 sheet: None (None), residues: 0 loop : 1.23 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.011 0.001 TYR A 168 ARG 0.001 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.407 Fit side-chains REVERT: A 200 MET cc_start: 0.7755 (mmt) cc_final: 0.7461 (mmp) REVERT: A 273 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7605 (m-80) REVERT: A 351 MET cc_start: 0.8652 (mtt) cc_final: 0.8387 (mtm) outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 0.1508 time to fit residues: 9.4353 Evaluate side-chains 47 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3572 Z= 0.234 Angle : 0.477 5.098 4870 Z= 0.247 Chirality : 0.037 0.123 562 Planarity : 0.004 0.031 601 Dihedral : 4.744 57.552 487 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.43 % Allowed : 9.43 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.41), residues: 443 helix: 2.28 (0.30), residues: 305 sheet: None (None), residues: 0 loop : 1.19 (0.57), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.004 0.001 HIS A 49 PHE 0.010 0.001 PHE A 32 TYR 0.011 0.001 TYR A 168 ARG 0.002 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.330 Fit side-chains REVERT: A 200 MET cc_start: 0.7749 (mmt) cc_final: 0.7490 (mmp) REVERT: A 273 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7654 (m-80) REVERT: A 351 MET cc_start: 0.8684 (mtt) cc_final: 0.8414 (mtm) outliers start: 9 outliers final: 7 residues processed: 47 average time/residue: 0.1500 time to fit residues: 9.0435 Evaluate side-chains 50 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 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 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3572 Z= 0.172 Angle : 0.437 5.113 4870 Z= 0.227 Chirality : 0.036 0.124 562 Planarity : 0.004 0.030 601 Dihedral : 4.656 58.331 487 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.70 % Allowed : 10.51 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.41), residues: 443 helix: 2.39 (0.30), residues: 306 sheet: None (None), residues: 0 loop : 1.15 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.004 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.011 0.001 TYR A 168 ARG 0.001 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 200 MET cc_start: 0.7762 (mmt) cc_final: 0.7498 (mmp) REVERT: A 273 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7533 (m-80) REVERT: A 351 MET cc_start: 0.8650 (mtt) cc_final: 0.8373 (mtm) REVERT: A 395 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.7134 (mm) outliers start: 10 outliers final: 7 residues processed: 50 average time/residue: 0.1471 time to fit residues: 9.4193 Evaluate side-chains 48 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7866 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3572 Z= 0.188 Angle : 0.443 5.028 4870 Z= 0.230 Chirality : 0.036 0.122 562 Planarity : 0.004 0.030 601 Dihedral : 4.678 59.795 487 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.23 % Allowed : 10.51 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.42), residues: 443 helix: 2.23 (0.30), residues: 312 sheet: None (None), residues: 0 loop : 1.32 (0.59), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 261 HIS 0.004 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.011 0.001 TYR A 168 ARG 0.001 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 43 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 200 MET cc_start: 0.7759 (mmt) cc_final: 0.7505 (mmp) REVERT: A 273 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7578 (m-80) REVERT: A 351 MET cc_start: 0.8651 (mtt) cc_final: 0.8370 (mtm) REVERT: A 395 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7139 (mm) outliers start: 12 outliers final: 7 residues processed: 52 average time/residue: 0.1399 time to fit residues: 9.2904 Evaluate side-chains 51 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 0.0000 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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: 0.7840 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3572 Z= 0.148 Angle : 0.417 5.042 4870 Z= 0.215 Chirality : 0.035 0.123 562 Planarity : 0.004 0.029 601 Dihedral : 4.596 59.828 487 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.96 % Allowed : 11.32 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.42), residues: 443 helix: 2.35 (0.30), residues: 312 sheet: None (None), residues: 0 loop : 1.35 (0.60), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.008 0.001 PHE A 355 TYR 0.010 0.001 TYR A 168 ARG 0.001 0.000 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 200 MET cc_start: 0.7771 (mmt) cc_final: 0.7507 (mmp) REVERT: A 273 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7503 (m-80) REVERT: A 351 MET cc_start: 0.8636 (mtt) cc_final: 0.8367 (mtm) REVERT: A 395 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.7107 (mm) outliers start: 11 outliers final: 7 residues processed: 54 average time/residue: 0.1406 time to fit residues: 9.7322 Evaluate side-chains 54 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7843 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3572 Z= 0.153 Angle : 0.426 5.785 4870 Z= 0.218 Chirality : 0.035 0.123 562 Planarity : 0.004 0.028 601 Dihedral : 4.544 59.026 487 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.96 % Allowed : 11.86 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.42), residues: 443 helix: 2.36 (0.30), residues: 312 sheet: None (None), residues: 0 loop : 1.34 (0.60), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.011 0.001 TYR A 168 ARG 0.001 0.000 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 27 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7042 (tt) REVERT: A 73 THR cc_start: 0.8348 (m) cc_final: 0.8036 (m) REVERT: A 200 MET cc_start: 0.7777 (mmt) cc_final: 0.7514 (mmp) REVERT: A 273 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7525 (m-80) REVERT: A 351 MET cc_start: 0.8634 (mtt) cc_final: 0.8367 (mtm) REVERT: A 395 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.7108 (mm) outliers start: 11 outliers final: 7 residues processed: 50 average time/residue: 0.1454 time to fit residues: 9.2929 Evaluate side-chains 52 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3572 Z= 0.151 Angle : 0.424 5.345 4870 Z= 0.217 Chirality : 0.035 0.123 562 Planarity : 0.004 0.028 601 Dihedral : 4.509 58.326 487 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.96 % Allowed : 11.59 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.42), residues: 443 helix: 2.37 (0.30), residues: 312 sheet: None (None), residues: 0 loop : 1.32 (0.60), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.010 0.001 TYR A 168 ARG 0.001 0.000 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.329 Fit side-chains REVERT: A 27 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7037 (tt) REVERT: A 73 THR cc_start: 0.8344 (m) cc_final: 0.8034 (m) REVERT: A 200 MET cc_start: 0.7772 (mmt) cc_final: 0.7505 (mmp) REVERT: A 273 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7474 (m-80) REVERT: A 351 MET cc_start: 0.8646 (mtt) cc_final: 0.8366 (mtm) REVERT: A 395 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.7209 (mm) outliers start: 11 outliers final: 7 residues processed: 50 average time/residue: 0.1500 time to fit residues: 9.5577 Evaluate side-chains 53 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.0370 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 0.0980 chunk 35 optimal weight: 0.6980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3572 Z= 0.137 Angle : 0.418 5.424 4870 Z= 0.214 Chirality : 0.035 0.123 562 Planarity : 0.004 0.028 601 Dihedral : 4.450 57.859 487 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.43 % Allowed : 12.13 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.42), residues: 443 helix: 2.43 (0.30), residues: 312 sheet: None (None), residues: 0 loop : 1.25 (0.60), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.008 0.001 PHE A 355 TYR 0.010 0.001 TYR A 168 ARG 0.002 0.000 ARG A 339 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.365 Fit side-chains REVERT: A 27 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7014 (tt) REVERT: A 73 THR cc_start: 0.8348 (m) cc_final: 0.8042 (m) REVERT: A 200 MET cc_start: 0.7690 (mmt) cc_final: 0.7416 (mmp) REVERT: A 273 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: A 351 MET cc_start: 0.8633 (mtt) cc_final: 0.8359 (mtm) REVERT: A 395 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7196 (mm) outliers start: 9 outliers final: 6 residues processed: 50 average time/residue: 0.1441 time to fit residues: 9.1824 Evaluate side-chains 52 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.0570 chunk 1 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 0.0870 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.190823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.136789 restraints weight = 3576.705| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.83 r_work: 0.3179 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3572 Z= 0.120 Angle : 0.405 5.298 4870 Z= 0.206 Chirality : 0.034 0.123 562 Planarity : 0.004 0.029 601 Dihedral : 4.387 57.431 487 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.43 % Allowed : 12.13 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.42), residues: 443 helix: 2.51 (0.30), residues: 312 sheet: None (None), residues: 0 loop : 1.25 (0.60), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.003 0.000 HIS A 49 PHE 0.008 0.001 PHE A 355 TYR 0.010 0.001 TYR A 168 ARG 0.001 0.000 ARG A 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1142.91 seconds wall clock time: 20 minutes 49.33 seconds (1249.33 seconds total)