Starting phenix.real_space_refine on Fri Jul 19 07:29:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubw_42107/07_2024/8ubw_42107_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubw_42107/07_2024/8ubw_42107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubw_42107/07_2024/8ubw_42107.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubw_42107/07_2024/8ubw_42107.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubw_42107/07_2024/8ubw_42107_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubw_42107/07_2024/8ubw_42107_trim.cif" } resolution = 2.59 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 18 5.16 5 C 2259 2.51 5 N 502 2.21 5 O 619 1.98 5 H 3343 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 136": "OE1" <-> "OE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 6741 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 6591 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 17, 'TRANS': 400} Chain: "A" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 150 Unusual residues: {'CHT': 1, 'Y01': 3} Classifications: {'undetermined': 4, 'water': 38} Link IDs: {None: 41} Time building chain proxies: 4.57, per 1000 atoms: 0.68 Number of scatterers: 6741 At special positions: 0 Unit cell: (84.1, 55.1, 65.975, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 O 619 8.00 N 502 7.00 C 2259 6.00 H 3343 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.17 Conformation dependent library (CDL) restraints added in 598.6 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 89.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 105 through 131 removed outlier: 3.981A pdb=" N VAL A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER A 129 " --> pdb=" O TRP A 125 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.730A pdb=" N ILE A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 5.021A pdb=" N PHE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 172 through 193 removed outlier: 3.870A pdb=" N THR A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 193 " --> pdb=" O TRP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 215 removed outlier: 3.649A pdb=" N THR A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 4.244A pdb=" N ARG A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 260 removed outlier: 3.512A pdb=" N ASN A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 266 through 296 Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 331 through 363 removed outlier: 5.147A pdb=" N ASN A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLN A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR A 362 " --> pdb=" O MET A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 396 Processing helix chain 'A' and resid 397 through 420 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 424 through 454 removed outlier: 3.500A pdb=" N VAL A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 443 " --> pdb=" O MET A 439 " (cutoff:3.500A) Proline residue: A 444 - end of helix Processing helix chain 'A' and resid 458 through 488 removed outlier: 3.516A pdb=" N SER A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 511 removed outlier: 3.868A pdb=" N GLY A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 816 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: 2.39 Time building geometry restraints manager: 6.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3335 1.03 - 1.23: 11 1.23 - 1.42: 1394 1.42 - 1.62: 2026 1.62 - 1.81: 28 Bond restraints: 6794 Sorted by residual: bond pdb=" N VAL A 195 " pdb=" CA VAL A 195 " ideal model delta sigma weight residual 1.474 1.459 0.016 1.57e-02 4.06e+03 1.01e+00 bond pdb=" CB ASN A 265 " pdb=" CG ASN A 265 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.57e-01 bond pdb=" C VAL A 260 " pdb=" O VAL A 260 " ideal model delta sigma weight residual 1.232 1.240 -0.008 1.01e-02 9.80e+03 6.33e-01 bond pdb=" N VAL A 260 " pdb=" CA VAL A 260 " ideal model delta sigma weight residual 1.456 1.462 -0.006 8.60e-03 1.35e+04 4.35e-01 bond pdb=" CB ASN A 331 " pdb=" CG ASN A 331 " ideal model delta sigma weight residual 1.516 1.532 -0.016 2.50e-02 1.60e+03 3.86e-01 ... (remaining 6789 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.71: 112 106.71 - 113.52: 7993 113.52 - 120.33: 2307 120.33 - 127.14: 1822 127.14 - 133.96: 36 Bond angle restraints: 12270 Sorted by residual: angle pdb=" N VAL A 195 " pdb=" CA VAL A 195 " pdb=" C VAL A 195 " ideal model delta sigma weight residual 106.21 109.73 -3.52 1.07e+00 8.73e-01 1.08e+01 angle pdb=" C ILE A 332 " pdb=" CA ILE A 332 " pdb=" CB ILE A 332 " ideal model delta sigma weight residual 114.00 110.64 3.36 1.31e+00 5.83e-01 6.57e+00 angle pdb=" C ASN A 331 " pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 120.33 122.28 -1.95 8.00e-01 1.56e+00 5.95e+00 angle pdb=" C VAL A 195 " pdb=" CA VAL A 195 " pdb=" CB VAL A 195 " ideal model delta sigma weight residual 113.22 110.82 2.40 1.12e+00 7.97e-01 4.60e+00 angle pdb=" CA VAL A 195 " pdb=" C VAL A 195 " pdb=" O VAL A 195 " ideal model delta sigma weight residual 122.63 120.87 1.76 8.70e-01 1.32e+00 4.08e+00 ... (remaining 12265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3034 17.95 - 35.91: 200 35.91 - 53.86: 100 53.86 - 71.82: 29 71.82 - 89.77: 3 Dihedral angle restraints: 3366 sinusoidal: 1889 harmonic: 1477 Sorted by residual: dihedral pdb=" CA LEU A 254 " pdb=" C LEU A 254 " pdb=" N LEU A 255 " pdb=" CA LEU A 255 " ideal model delta harmonic sigma weight residual 180.00 -163.65 -16.35 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB MET A 358 " pdb=" CG MET A 358 " pdb=" SD MET A 358 " pdb=" CE MET A 358 " ideal model delta sinusoidal sigma weight residual 60.00 5.96 54.04 3 1.50e+01 4.44e-03 9.25e+00 dihedral pdb=" CA ARG A 372 " pdb=" CB ARG A 372 " pdb=" CG ARG A 372 " pdb=" CD ARG A 372 " ideal model delta sinusoidal sigma weight residual -180.00 -129.13 -50.87 3 1.50e+01 4.44e-03 8.95e+00 ... (remaining 3363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 374 0.023 - 0.045: 103 0.045 - 0.067: 44 0.067 - 0.090: 38 0.090 - 0.112: 9 Chirality restraints: 568 Sorted by residual: chirality pdb=" CA PRO A 333 " pdb=" N PRO A 333 " pdb=" C PRO A 333 " pdb=" CB PRO A 333 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.16e-01 chirality pdb=" CA ASN A 331 " pdb=" N ASN A 331 " pdb=" C ASN A 331 " pdb=" CB ASN A 331 " both_signs ideal model delta sigma weight residual False 2.51 2.62 -0.11 2.00e-01 2.50e+01 3.12e-01 chirality pdb=" CA PRO A 221 " pdb=" N PRO A 221 " pdb=" C PRO A 221 " pdb=" CB PRO A 221 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.00e-01 ... (remaining 565 not shown) Planarity restraints: 957 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 114 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C PHE A 114 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE A 114 " 0.010 2.00e-02 2.50e+03 pdb=" N SER A 115 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 230 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO A 231 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.005 2.00e-02 2.50e+03 9.06e-03 1.23e+00 pdb=" CG ASN A 331 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 331 " -0.003 2.00e-02 2.50e+03 pdb="HD22 ASN A 331 " -0.001 2.00e-02 2.50e+03 ... (remaining 954 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 931 2.26 - 2.85: 15618 2.85 - 3.43: 18994 3.43 - 4.02: 25823 4.02 - 4.60: 39249 Nonbonded interactions: 100615 Sorted by model distance: nonbonded pdb=" O ILE A 415 " pdb=" HG1 THR A 419 " model vdw 1.679 1.850 nonbonded pdb=" HG SER A 350 " pdb=" OE1 GLN A 481 " model vdw 1.699 1.850 nonbonded pdb=" HH TYR A 349 " pdb=" O HOH A 702 " model vdw 1.736 1.850 nonbonded pdb=" HH TYR A 139 " pdb=" O SER A 194 " model vdw 1.750 1.850 nonbonded pdb=" H GLY A 219 " pdb=" O HOH A 707 " model vdw 1.762 1.850 ... (remaining 100610 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: 9.190 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: 0.100 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 27.330 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3451 Z= 0.133 Angle : 0.476 4.974 4724 Z= 0.269 Chirality : 0.033 0.112 568 Planarity : 0.003 0.029 557 Dihedral : 14.624 89.769 1369 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.85 % Allowed : 14.41 % Favored : 84.75 % 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: 3.39 (0.42), residues: 416 helix: 3.09 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -1.68 (0.55), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 201 HIS 0.001 0.000 HIS A 145 PHE 0.012 0.001 PHE A 496 TYR 0.015 0.001 TYR A 117 ARG 0.005 0.001 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 TYR cc_start: 0.7974 (m-80) cc_final: 0.7672 (m-80) REVERT: A 459 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6840 (tm-30) outliers start: 3 outliers final: 1 residues processed: 46 average time/residue: 2.2534 time to fit residues: 107.2897 Evaluate side-chains 34 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.0170 chunk 32 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3451 Z= 0.153 Angle : 0.484 5.690 4724 Z= 0.252 Chirality : 0.034 0.116 568 Planarity : 0.004 0.032 557 Dihedral : 5.531 55.172 664 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.13 % Allowed : 14.41 % Favored : 84.46 % 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: 3.79 (0.41), residues: 416 helix: 3.24 (0.27), residues: 342 sheet: None (None), residues: 0 loop : -1.40 (0.60), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 500 HIS 0.000 0.000 HIS A 145 PHE 0.014 0.001 PHE A 496 TYR 0.022 0.001 TYR A 117 ARG 0.003 0.001 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6840 (tm-30) outliers start: 4 outliers final: 2 residues processed: 40 average time/residue: 2.2612 time to fit residues: 93.7117 Evaluate side-chains 33 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 392 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3451 Z= 0.241 Angle : 0.501 5.568 4724 Z= 0.267 Chirality : 0.035 0.140 568 Planarity : 0.004 0.031 557 Dihedral : 5.780 50.233 664 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.13 % Allowed : 14.41 % Favored : 84.46 % 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: 3.66 (0.41), residues: 416 helix: 3.08 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.50 (0.63), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 201 HIS 0.001 0.000 HIS A 145 PHE 0.016 0.002 PHE A 496 TYR 0.026 0.001 TYR A 117 ARG 0.005 0.001 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 33 average time/residue: 1.9422 time to fit residues: 67.0087 Evaluate side-chains 29 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3451 Z= 0.263 Angle : 0.495 5.520 4724 Z= 0.264 Chirality : 0.035 0.134 568 Planarity : 0.004 0.032 557 Dihedral : 5.569 46.258 662 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.56 % Allowed : 16.10 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.41), residues: 416 helix: 3.06 (0.27), residues: 347 sheet: None (None), residues: 0 loop : -1.32 (0.62), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 201 HIS 0.001 0.000 HIS A 145 PHE 0.015 0.001 PHE A 496 TYR 0.023 0.001 TYR A 117 ARG 0.003 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.414 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 31 average time/residue: 1.9764 time to fit residues: 63.8487 Evaluate side-chains 27 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.0570 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3451 Z= 0.189 Angle : 0.482 5.333 4724 Z= 0.256 Chirality : 0.034 0.127 568 Planarity : 0.004 0.032 557 Dihedral : 5.438 45.835 662 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.85 % Allowed : 15.54 % Favored : 83.62 % 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: 3.64 (0.41), residues: 416 helix: 3.09 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.62 (0.63), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.000 0.000 HIS A 145 PHE 0.013 0.001 PHE A 496 TYR 0.023 0.001 TYR A 117 ARG 0.003 0.000 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.453 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 30 average time/residue: 2.1844 time to fit residues: 68.3399 Evaluate side-chains 29 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.0670 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.0980 chunk 4 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 overall best weight: 0.3718 ------------------------------------------------------------------------------- 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: 0.8865 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3451 Z= 0.152 Angle : 0.459 5.165 4724 Z= 0.242 Chirality : 0.034 0.123 568 Planarity : 0.004 0.031 557 Dihedral : 5.161 44.434 662 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.56 % Allowed : 16.38 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.82 (0.41), residues: 416 helix: 3.23 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.65 (0.63), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 500 HIS 0.000 0.000 HIS A 145 PHE 0.012 0.001 PHE A 496 TYR 0.023 0.001 TYR A 117 ARG 0.002 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.659 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 28 average time/residue: 2.0502 time to fit residues: 60.0600 Evaluate side-chains 28 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 23 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3451 Z= 0.206 Angle : 0.478 5.464 4724 Z= 0.253 Chirality : 0.035 0.128 568 Planarity : 0.004 0.038 557 Dihedral : 5.217 41.041 662 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.13 % Allowed : 15.25 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.41), residues: 416 helix: 3.19 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.71 (0.63), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 500 HIS 0.000 0.000 HIS A 145 PHE 0.014 0.001 PHE A 496 TYR 0.024 0.001 TYR A 117 ARG 0.003 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8300 (mt) REVERT: A 447 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8165 (t80) outliers start: 4 outliers final: 1 residues processed: 29 average time/residue: 2.1561 time to fit residues: 65.2391 Evaluate side-chains 30 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 447 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8897 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3451 Z= 0.208 Angle : 0.478 5.350 4724 Z= 0.253 Chirality : 0.035 0.129 568 Planarity : 0.004 0.031 557 Dihedral : 5.181 36.998 662 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.85 % Allowed : 15.82 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.41), residues: 416 helix: 3.17 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.65 (0.64), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.001 0.000 HIS A 198 PHE 0.014 0.001 PHE A 496 TYR 0.022 0.001 TYR A 117 ARG 0.001 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 392 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8279 (mt) REVERT: A 447 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8178 (t80) outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 2.0711 time to fit residues: 60.6218 Evaluate side-chains 29 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 447 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 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: 0.8890 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3451 Z= 0.181 Angle : 0.473 5.397 4724 Z= 0.249 Chirality : 0.034 0.127 568 Planarity : 0.004 0.032 557 Dihedral : 5.106 35.678 662 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.85 % Allowed : 15.82 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.41), residues: 416 helix: 3.18 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.65 (0.65), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.000 0.000 HIS A 145 PHE 0.013 0.001 PHE A 496 TYR 0.023 0.001 TYR A 117 ARG 0.003 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 392 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8247 (mt) REVERT: A 447 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8179 (t80) outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 2.0361 time to fit residues: 59.6219 Evaluate side-chains 29 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 447 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 0.1980 chunk 6 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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: 0.8879 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3451 Z= 0.161 Angle : 0.468 5.330 4724 Z= 0.247 Chirality : 0.034 0.125 568 Planarity : 0.005 0.042 557 Dihedral : 5.045 34.877 662 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.85 % Allowed : 15.82 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.81 (0.41), residues: 416 helix: 3.22 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.66 (0.65), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.000 0.000 HIS A 145 PHE 0.013 0.001 PHE A 496 TYR 0.025 0.001 TYR A 302 ARG 0.004 0.001 ARG A 516 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 392 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8232 (mt) REVERT: A 447 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8175 (t80) outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 2.0290 time to fit residues: 59.3804 Evaluate side-chains 30 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 447 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.0980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.0000 chunk 15 optimal weight: 0.0980 chunk 40 optimal weight: 0.0970 overall best weight: 0.2182 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.096414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.077863 restraints weight = 16157.525| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.09 r_work: 0.2863 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3451 Z= 0.128 Angle : 0.451 4.982 4724 Z= 0.236 Chirality : 0.033 0.118 568 Planarity : 0.004 0.031 557 Dihedral : 4.796 34.114 662 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.85 % Allowed : 16.10 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.95 (0.41), residues: 416 helix: 3.32 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.66 (0.65), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 500 HIS 0.000 0.000 HIS A 145 PHE 0.011 0.001 PHE A 496 TYR 0.023 0.001 TYR A 117 ARG 0.003 0.000 ARG A 301 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3242.19 seconds wall clock time: 56 minutes 59.25 seconds (3419.25 seconds total)