Starting phenix.real_space_refine on Thu Nov 14 02:09:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3g_41861/11_2024/8u3g_41861.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3g_41861/11_2024/8u3g_41861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3g_41861/11_2024/8u3g_41861.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3g_41861/11_2024/8u3g_41861.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3g_41861/11_2024/8u3g_41861.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3g_41861/11_2024/8u3g_41861.cif" } resolution = 3.42 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= 0.002 sd= 0.067 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 15 5.16 5 C 2241 2.51 5 N 524 2.21 5 O 579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3359 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3338 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 18, 'TRANS': 408} Chain breaks: 1 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {'ACE': 1} Classifications: {'peptide': 2, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 1} Time building chain proxies: 3.27, per 1000 atoms: 0.97 Number of scatterers: 3359 At special positions: 0 Unit cell: (59.76, 77.19, 81.34, 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 15 16.00 O 579 8.00 N 524 7.00 C 2241 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: 1.04 Conformation dependent library (CDL) restraints added in 397.5 milliseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 86.9% 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 38 through 64 removed outlier: 4.895A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N SER A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 114 through 122 removed outlier: 3.768A pdb=" N THR A 122 " --> pdb=" O GLY A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.544A pdb=" N GLY A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 160 removed outlier: 4.058A pdb=" N THR A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Proline residue: A 154 - end of helix removed outlier: 3.840A pdb=" N ASP A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 176 Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.524A pdb=" N ALA A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 194 through 224 removed outlier: 3.613A pdb=" N LEU A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 226 through 247 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.702A pdb=" N HIS A 255 " --> pdb=" O PRO A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 276 removed outlier: 4.041A pdb=" N ASN A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 319 removed outlier: 3.525A pdb=" N TRP A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 324 through 356 Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 357 through 360 Processing helix chain 'A' and resid 361 through 385 Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 388 through 402 removed outlier: 3.781A pdb=" N ALA A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 393 " --> pdb=" O TYR A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 412 removed outlier: 4.570A pdb=" N CYS A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.906A pdb=" N ALA A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 447 removed outlier: 3.728A pdb=" N THR A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Proline residue: A 436 - end of helix Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 452 through 477 removed outlier: 3.515A pdb=" N VAL A 459 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 729 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: 0.94 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 499 1.30 - 1.43: 1005 1.43 - 1.55: 1932 1.55 - 1.68: 0 1.68 - 1.81: 24 Bond restraints: 3460 Sorted by residual: bond pdb=" C ASP A 502 " pdb=" N GLU A 503 " ideal model delta sigma weight residual 1.329 1.455 -0.126 1.40e-02 5.10e+03 8.05e+01 bond pdb=" C ACE A 501 " pdb=" N ASP A 502 " ideal model delta sigma weight residual 1.329 1.445 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C ASP A 502 " pdb=" O ASP A 502 " ideal model delta sigma weight residual 1.231 1.177 0.054 2.00e-02 2.50e+03 7.33e+00 bond pdb=" CA SER A 331 " pdb=" CB SER A 331 " ideal model delta sigma weight residual 1.534 1.491 0.043 1.58e-02 4.01e+03 7.27e+00 bond pdb=" N ILE A 44 " pdb=" CA ILE A 44 " ideal model delta sigma weight residual 1.462 1.492 -0.030 1.14e-02 7.69e+03 7.01e+00 ... (remaining 3455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 4524 1.61 - 3.21: 148 3.21 - 4.82: 38 4.82 - 6.43: 8 6.43 - 8.03: 2 Bond angle restraints: 4720 Sorted by residual: angle pdb=" N SER A 331 " pdb=" CA SER A 331 " pdb=" C SER A 331 " ideal model delta sigma weight residual 113.50 105.63 7.87 1.23e+00 6.61e-01 4.09e+01 angle pdb=" CA ASP A 502 " pdb=" CB ASP A 502 " pdb=" CG ASP A 502 " ideal model delta sigma weight residual 112.60 117.30 -4.70 1.00e+00 1.00e+00 2.21e+01 angle pdb=" CA ILE A 44 " pdb=" C ILE A 44 " pdb=" O ILE A 44 " ideal model delta sigma weight residual 121.27 117.34 3.93 1.04e+00 9.25e-01 1.42e+01 angle pdb=" N ASN A 327 " pdb=" CA ASN A 327 " pdb=" C ASN A 327 " ideal model delta sigma weight residual 111.07 107.60 3.47 1.07e+00 8.73e-01 1.05e+01 angle pdb=" N VAL A 324 " pdb=" CA VAL A 324 " pdb=" C VAL A 324 " ideal model delta sigma weight residual 111.81 109.08 2.73 8.60e-01 1.35e+00 1.01e+01 ... (remaining 4715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 1755 17.81 - 35.62: 163 35.62 - 53.43: 26 53.43 - 71.24: 4 71.24 - 89.05: 2 Dihedral angle restraints: 1950 sinusoidal: 724 harmonic: 1226 Sorted by residual: dihedral pdb=" CA TRP A 103 " pdb=" C TRP A 103 " pdb=" N ASP A 104 " pdb=" CA ASP A 104 " ideal model delta harmonic sigma weight residual -180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE A 116 " pdb=" C PHE A 116 " pdb=" N TYR A 117 " pdb=" CA TYR A 117 " ideal model delta harmonic sigma weight residual 180.00 162.22 17.78 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA SER A 411 " pdb=" C SER A 411 " pdb=" N ILE A 412 " pdb=" CA ILE A 412 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 1947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 279 0.030 - 0.059: 161 0.059 - 0.089: 71 0.089 - 0.119: 18 0.119 - 0.148: 6 Chirality restraints: 535 Sorted by residual: chirality pdb=" CB VAL A 177 " pdb=" CA VAL A 177 " pdb=" CG1 VAL A 177 " pdb=" CG2 VAL A 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CG LEU A 60 " pdb=" CB LEU A 60 " pdb=" CD1 LEU A 60 " pdb=" CD2 LEU A 60 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA VAL A 482 " pdb=" N VAL A 482 " pdb=" C VAL A 482 " pdb=" CB VAL A 482 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 532 not shown) Planarity restraints: 574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 330 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C LEU A 330 " -0.031 2.00e-02 2.50e+03 pdb=" O LEU A 330 " 0.012 2.00e-02 2.50e+03 pdb=" N SER A 331 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 333 " -0.027 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO A 334 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 334 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 334 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 440 " -0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO A 441 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 441 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 441 " -0.020 5.00e-02 4.00e+02 ... (remaining 571 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 474 2.75 - 3.29: 3484 3.29 - 3.82: 5789 3.82 - 4.36: 6775 4.36 - 4.90: 11550 Nonbonded interactions: 28072 Sorted by model distance: nonbonded pdb=" O THR A 397 " pdb=" OG1 THR A 401 " model vdw 2.209 3.040 nonbonded pdb=" NH2 ARG A 364 " pdb=" OD2 ASP A 416 " model vdw 2.211 3.120 nonbonded pdb=" O SER A 213 " pdb=" OG SER A 217 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR A 40 " pdb=" OE2 GLU A 194 " model vdw 2.287 3.040 nonbonded pdb=" NH1 ARG A 39 " pdb=" OE2 GLU A 262 " model vdw 2.291 3.120 ... (remaining 28067 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: 1.520 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.630 Find NCS groups from input model: 0.030 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.006 0.126 3460 Z= 0.382 Angle : 0.734 8.032 4720 Z= 0.423 Chirality : 0.044 0.148 535 Planarity : 0.005 0.040 574 Dihedral : 13.981 89.049 1170 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % 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: -3.18 (0.35), residues: 423 helix: -1.46 (0.24), residues: 337 sheet: None (None), residues: 0 loop : -4.17 (0.50), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 244 HIS 0.004 0.001 HIS A 414 PHE 0.013 0.001 PHE A 232 TYR 0.013 0.001 TYR A 119 ARG 0.002 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.353 Fit side-chains REVERT: A 54 TYR cc_start: 0.8149 (m-10) cc_final: 0.7789 (m-80) REVERT: A 106 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8556 (tm-30) REVERT: A 119 TYR cc_start: 0.7920 (t80) cc_final: 0.7685 (t80) REVERT: A 257 ARG cc_start: 0.8163 (ptt-90) cc_final: 0.7823 (mtm-85) REVERT: A 321 ARG cc_start: 0.8482 (mmm160) cc_final: 0.7617 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1573 time to fit residues: 12.6806 Evaluate side-chains 56 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 0.1980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 457 GLN A 467 ASN A 483 GLN A 484 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3460 Z= 0.252 Angle : 0.630 7.273 4720 Z= 0.321 Chirality : 0.044 0.278 535 Planarity : 0.005 0.039 574 Dihedral : 5.398 44.184 459 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.54 % Allowed : 11.58 % Favored : 85.88 % 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: -1.45 (0.39), residues: 423 helix: -0.28 (0.27), residues: 347 sheet: None (None), residues: 0 loop : -3.75 (0.56), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 244 HIS 0.006 0.002 HIS A 414 PHE 0.014 0.001 PHE A 116 TYR 0.007 0.001 TYR A 335 ARG 0.002 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.357 Fit side-chains REVERT: A 54 TYR cc_start: 0.8080 (m-10) cc_final: 0.7774 (m-80) REVERT: A 66 ASP cc_start: 0.8504 (t0) cc_final: 0.8261 (t0) REVERT: A 257 ARG cc_start: 0.8113 (ptt-90) cc_final: 0.7875 (mtm-85) REVERT: A 321 ARG cc_start: 0.8468 (mmm160) cc_final: 0.7562 (ttp-170) REVERT: A 416 ASP cc_start: 0.8158 (m-30) cc_final: 0.7363 (m-30) outliers start: 9 outliers final: 8 residues processed: 58 average time/residue: 0.1362 time to fit residues: 10.2044 Evaluate side-chains 61 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 0.0010 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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: 0.7738 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3460 Z= 0.234 Angle : 0.617 6.225 4720 Z= 0.313 Chirality : 0.044 0.304 535 Planarity : 0.005 0.039 574 Dihedral : 5.288 39.839 459 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.95 % Allowed : 14.97 % Favored : 81.07 % 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: -0.77 (0.40), residues: 423 helix: 0.19 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -3.62 (0.56), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 456 HIS 0.005 0.002 HIS A 414 PHE 0.013 0.001 PHE A 47 TYR 0.008 0.001 TYR A 335 ARG 0.001 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.385 Fit side-chains REVERT: A 54 TYR cc_start: 0.8092 (m-10) cc_final: 0.7836 (m-80) REVERT: A 257 ARG cc_start: 0.8079 (ptt-90) cc_final: 0.7840 (mtm-85) REVERT: A 321 ARG cc_start: 0.8464 (mmm160) cc_final: 0.7544 (ttp-170) REVERT: A 416 ASP cc_start: 0.8053 (m-30) cc_final: 0.7198 (m-30) outliers start: 14 outliers final: 11 residues processed: 59 average time/residue: 0.1393 time to fit residues: 10.4178 Evaluate side-chains 62 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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: 0.7713 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3460 Z= 0.221 Angle : 0.606 5.884 4720 Z= 0.307 Chirality : 0.043 0.274 535 Planarity : 0.005 0.039 574 Dihedral : 5.149 35.800 459 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.24 % Allowed : 16.38 % Favored : 79.38 % 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: -0.38 (0.40), residues: 423 helix: 0.45 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -3.48 (0.57), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 244 HIS 0.005 0.002 HIS A 414 PHE 0.013 0.001 PHE A 47 TYR 0.008 0.001 TYR A 335 ARG 0.001 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.362 Fit side-chains REVERT: A 54 TYR cc_start: 0.8082 (m-10) cc_final: 0.7759 (m-80) REVERT: A 257 ARG cc_start: 0.8064 (ptt-90) cc_final: 0.7834 (mtm-85) REVERT: A 321 ARG cc_start: 0.8494 (mmm160) cc_final: 0.7483 (ttp-170) REVERT: A 416 ASP cc_start: 0.8066 (m-30) cc_final: 0.7584 (m-30) outliers start: 15 outliers final: 13 residues processed: 61 average time/residue: 0.1432 time to fit residues: 11.0834 Evaluate side-chains 65 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7732 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3460 Z= 0.252 Angle : 0.620 7.836 4720 Z= 0.312 Chirality : 0.043 0.259 535 Planarity : 0.005 0.040 574 Dihedral : 5.133 35.515 459 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.95 % Allowed : 17.80 % Favored : 78.25 % 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: -0.27 (0.41), residues: 423 helix: 0.52 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -3.42 (0.58), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.004 0.002 HIS A 298 PHE 0.013 0.001 PHE A 116 TYR 0.007 0.001 TYR A 335 ARG 0.002 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.366 Fit side-chains REVERT: A 54 TYR cc_start: 0.8076 (m-10) cc_final: 0.7745 (m-80) REVERT: A 257 ARG cc_start: 0.8080 (ptt-90) cc_final: 0.7846 (mtm-85) REVERT: A 321 ARG cc_start: 0.8497 (mmm160) cc_final: 0.7492 (ttp-170) REVERT: A 416 ASP cc_start: 0.8045 (m-30) cc_final: 0.7464 (m-30) outliers start: 14 outliers final: 13 residues processed: 63 average time/residue: 0.1433 time to fit residues: 11.5801 Evaluate side-chains 68 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 0.0970 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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: 0.7699 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3460 Z= 0.226 Angle : 0.614 6.769 4720 Z= 0.309 Chirality : 0.044 0.273 535 Planarity : 0.005 0.042 574 Dihedral : 5.008 29.420 459 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.95 % Allowed : 19.21 % Favored : 76.84 % 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: -0.07 (0.41), residues: 423 helix: 0.64 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -3.26 (0.58), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 485 HIS 0.004 0.001 HIS A 298 PHE 0.013 0.001 PHE A 47 TYR 0.008 0.001 TYR A 335 ARG 0.002 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.336 Fit side-chains REVERT: A 54 TYR cc_start: 0.8007 (m-10) cc_final: 0.7777 (m-80) REVERT: A 257 ARG cc_start: 0.8083 (ptt-90) cc_final: 0.7798 (mtm-85) REVERT: A 321 ARG cc_start: 0.8495 (mmm160) cc_final: 0.7492 (ttp-170) REVERT: A 410 PHE cc_start: 0.5640 (t80) cc_final: 0.5110 (t80) REVERT: A 416 ASP cc_start: 0.8009 (m-30) cc_final: 0.7351 (m-30) outliers start: 14 outliers final: 13 residues processed: 60 average time/residue: 0.1439 time to fit residues: 10.8860 Evaluate side-chains 64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.0370 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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: 0.7682 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3460 Z= 0.212 Angle : 0.600 5.888 4720 Z= 0.304 Chirality : 0.042 0.230 535 Planarity : 0.005 0.041 574 Dihedral : 4.907 24.267 459 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.24 % Allowed : 19.49 % Favored : 76.27 % 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: 0.14 (0.41), residues: 423 helix: 0.80 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -3.30 (0.59), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 485 HIS 0.004 0.001 HIS A 298 PHE 0.013 0.001 PHE A 47 TYR 0.015 0.001 TYR A 128 ARG 0.002 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.343 Fit side-chains REVERT: A 54 TYR cc_start: 0.8061 (m-10) cc_final: 0.7783 (m-80) REVERT: A 257 ARG cc_start: 0.8092 (ptt-90) cc_final: 0.7817 (mtm-85) REVERT: A 321 ARG cc_start: 0.8495 (mmm160) cc_final: 0.7493 (ttp-170) REVERT: A 410 PHE cc_start: 0.5510 (t80) cc_final: 0.5026 (t80) REVERT: A 416 ASP cc_start: 0.7949 (m-30) cc_final: 0.7282 (m-30) outliers start: 15 outliers final: 12 residues processed: 60 average time/residue: 0.1392 time to fit residues: 10.6332 Evaluate side-chains 63 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 0.0980 chunk 34 optimal weight: 0.9980 overall best weight: 0.3758 ------------------------------------------------------------------------------- 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: 0.7629 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3460 Z= 0.189 Angle : 0.590 6.048 4720 Z= 0.299 Chirality : 0.041 0.186 535 Planarity : 0.005 0.042 574 Dihedral : 4.782 22.864 459 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.39 % Allowed : 20.90 % Favored : 75.71 % 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: 0.41 (0.42), residues: 423 helix: 1.01 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -3.25 (0.58), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 485 HIS 0.004 0.001 HIS A 298 PHE 0.014 0.001 PHE A 47 TYR 0.009 0.001 TYR A 335 ARG 0.001 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.353 Fit side-chains REVERT: A 54 TYR cc_start: 0.8065 (m-10) cc_final: 0.7700 (m-80) REVERT: A 257 ARG cc_start: 0.8070 (ptt-90) cc_final: 0.7838 (mtm-85) REVERT: A 321 ARG cc_start: 0.8491 (mmm160) cc_final: 0.7489 (ttp-170) REVERT: A 410 PHE cc_start: 0.5316 (t80) cc_final: 0.4860 (t80) REVERT: A 416 ASP cc_start: 0.7931 (m-30) cc_final: 0.7252 (m-30) outliers start: 12 outliers final: 10 residues processed: 59 average time/residue: 0.1402 time to fit residues: 10.5379 Evaluate side-chains 63 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.0970 chunk 41 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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: 0.7662 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3460 Z= 0.219 Angle : 0.602 5.899 4720 Z= 0.304 Chirality : 0.042 0.192 535 Planarity : 0.005 0.042 574 Dihedral : 4.792 23.036 459 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.11 % Allowed : 22.03 % Favored : 74.86 % 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: 0.43 (0.41), residues: 423 helix: 1.00 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -3.23 (0.59), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 485 HIS 0.005 0.001 HIS A 298 PHE 0.013 0.001 PHE A 47 TYR 0.016 0.001 TYR A 128 ARG 0.002 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.339 Fit side-chains REVERT: A 54 TYR cc_start: 0.8116 (m-10) cc_final: 0.7701 (m-80) REVERT: A 257 ARG cc_start: 0.8089 (ptt-90) cc_final: 0.7835 (mtm-85) REVERT: A 321 ARG cc_start: 0.8496 (mmm160) cc_final: 0.7501 (ttp-170) REVERT: A 410 PHE cc_start: 0.5315 (t80) cc_final: 0.4858 (t80) REVERT: A 416 ASP cc_start: 0.7928 (m-30) cc_final: 0.7231 (m-30) outliers start: 11 outliers final: 11 residues processed: 58 average time/residue: 0.1423 time to fit residues: 10.5787 Evaluate side-chains 63 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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: 0.7662 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3460 Z= 0.218 Angle : 0.608 6.480 4720 Z= 0.306 Chirality : 0.043 0.192 535 Planarity : 0.005 0.043 574 Dihedral : 4.782 22.973 459 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.39 % Allowed : 22.03 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.41), residues: 423 helix: 1.05 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -3.18 (0.58), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 485 HIS 0.004 0.001 HIS A 298 PHE 0.013 0.001 PHE A 47 TYR 0.007 0.001 TYR A 335 ARG 0.002 0.000 ARG A 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.373 Fit side-chains REVERT: A 54 TYR cc_start: 0.8112 (m-10) cc_final: 0.7692 (m-80) REVERT: A 257 ARG cc_start: 0.8109 (ptt-90) cc_final: 0.7873 (mtm-85) REVERT: A 321 ARG cc_start: 0.8493 (mmm160) cc_final: 0.7505 (ttp-170) REVERT: A 410 PHE cc_start: 0.5316 (t80) cc_final: 0.4867 (t80) REVERT: A 416 ASP cc_start: 0.7935 (m-30) cc_final: 0.7293 (m-30) outliers start: 12 outliers final: 10 residues processed: 60 average time/residue: 0.1590 time to fit residues: 12.1672 Evaluate side-chains 61 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 482 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.0030 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.162032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116973 restraints weight = 4009.066| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.38 r_work: 0.3250 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3460 Z= 0.246 Angle : 0.619 5.928 4720 Z= 0.312 Chirality : 0.043 0.207 535 Planarity : 0.005 0.039 574 Dihedral : 4.824 23.196 459 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.82 % Allowed : 22.88 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.41), residues: 423 helix: 0.98 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -3.20 (0.60), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 485 HIS 0.004 0.001 HIS A 298 PHE 0.014 0.001 PHE A 116 TYR 0.016 0.001 TYR A 128 ARG 0.002 0.000 ARG A 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1144.08 seconds wall clock time: 21 minutes 47.52 seconds (1307.52 seconds total)