Starting phenix.real_space_refine on Thu Jul 18 18:51:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtv_36653/07_2024/8jtv_36653.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtv_36653/07_2024/8jtv_36653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtv_36653/07_2024/8jtv_36653.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtv_36653/07_2024/8jtv_36653.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtv_36653/07_2024/8jtv_36653.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtv_36653/07_2024/8jtv_36653.cif" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.107 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 27 5.16 5 C 2010 2.51 5 N 505 2.21 5 O 525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3067 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3058 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 21, 'TRANS': 415} Chain breaks: 2 Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 426 Unresolved non-hydrogen dihedrals: 276 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 211 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'MF8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.45, per 1000 atoms: 0.80 Number of scatterers: 3067 At special positions: 0 Unit cell: (70.3625, 88.765, 64.95, 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 27 16.00 O 525 8.00 N 505 7.00 C 2010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 705.5 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 800 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 1 sheets defined 78.3% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.804A pdb=" N ILE A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 36 through 43 Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.556A pdb=" N GLU A 57 " --> pdb=" O PRO A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 4.090A pdb=" N VAL A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.551A pdb=" N LEU A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 144 through 173 removed outlier: 3.703A pdb=" N LEU A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 Processing helix chain 'A' and resid 198 through 228 removed outlier: 3.752A pdb=" N VAL A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 258 Processing helix chain 'A' and resid 260 through 273 Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 340 through 372 removed outlier: 3.653A pdb=" N ARG A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 385 through 397 removed outlier: 3.880A pdb=" N GLY A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 423 removed outlier: 3.658A pdb=" N ALA A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 457 removed outlier: 3.701A pdb=" N ALA A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 457 " --> pdb=" O ASN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 488 removed outlier: 3.560A pdb=" N LEU A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) Proline residue: A 481 - end of helix removed outlier: 4.019A pdb=" N ARG A 486 " --> pdb=" O PHE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 510 removed outlier: 4.456A pdb=" N LEU A 496 " --> pdb=" O GLN A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50 243 hydrogen bonds defined for protein. 717 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: 0.71 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 961 1.34 - 1.46: 688 1.46 - 1.58: 1451 1.58 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 3139 Sorted by residual: bond pdb=" C07 MF8 A 601 " pdb=" N08 MF8 A 601 " ideal model delta sigma weight residual 1.281 1.451 -0.170 2.00e-02 2.50e+03 7.19e+01 bond pdb=" C07 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 1.393 1.252 0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C04 MF8 A 601 " pdb=" N02 MF8 A 601 " ideal model delta sigma weight residual 1.362 1.444 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C07 MF8 A 601 " pdb=" N09 MF8 A 601 " ideal model delta sigma weight residual 1.358 1.439 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C04 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 1.387 1.451 -0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 3134 not shown) Histogram of bond angle deviations from ideal: 99.48 - 106.53: 107 106.53 - 113.58: 1727 113.58 - 120.62: 1421 120.62 - 127.67: 1011 127.67 - 134.72: 39 Bond angle restraints: 4305 Sorted by residual: angle pdb=" N VAL A 103 " pdb=" CA VAL A 103 " pdb=" C VAL A 103 " ideal model delta sigma weight residual 111.56 104.18 7.38 8.60e-01 1.35e+00 7.37e+01 angle pdb=" C VAL A 103 " pdb=" CA VAL A 103 " pdb=" CB VAL A 103 " ideal model delta sigma weight residual 111.44 116.67 -5.23 9.50e-01 1.11e+00 3.03e+01 angle pdb=" N ASP A 104 " pdb=" CA ASP A 104 " pdb=" CB ASP A 104 " ideal model delta sigma weight residual 111.09 105.80 5.29 1.24e+00 6.50e-01 1.82e+01 angle pdb=" N02 MF8 A 601 " pdb=" C04 MF8 A 601 " pdb=" N05 MF8 A 601 " ideal model delta sigma weight residual 126.24 117.99 8.25 3.00e+00 1.11e-01 7.57e+00 angle pdb=" N ILE A 483 " pdb=" CA ILE A 483 " pdb=" C ILE A 483 " ideal model delta sigma weight residual 111.81 109.50 2.31 8.60e-01 1.35e+00 7.20e+00 ... (remaining 4300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.71: 1617 13.71 - 27.42: 127 27.42 - 41.13: 54 41.13 - 54.84: 4 54.84 - 68.56: 4 Dihedral angle restraints: 1806 sinusoidal: 560 harmonic: 1246 Sorted by residual: dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual 93.00 24.44 68.56 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual 93.00 160.55 -67.55 1 1.00e+01 1.00e-02 5.93e+01 dihedral pdb=" CA LEU A 140 " pdb=" C LEU A 140 " pdb=" N VAL A 141 " pdb=" CA VAL A 141 " ideal model delta harmonic sigma weight residual -180.00 -163.67 -16.33 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 1803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 290 0.025 - 0.050: 143 0.050 - 0.076: 56 0.076 - 0.101: 27 0.101 - 0.126: 8 Chirality restraints: 524 Sorted by residual: chirality pdb=" CB VAL A 385 " pdb=" CA VAL A 385 " pdb=" CG1 VAL A 385 " pdb=" CG2 VAL A 385 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA THR A 480 " pdb=" N THR A 480 " pdb=" C THR A 480 " pdb=" CB THR A 480 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.34e-01 chirality pdb=" CA LEU A 494 " pdb=" N LEU A 494 " pdb=" C LEU A 494 " pdb=" CB LEU A 494 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.98e-01 ... (remaining 521 not shown) Planarity restraints: 540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 MF8 A 601 " 0.078 2.00e-02 2.50e+03 6.73e-02 1.02e+02 pdb=" C03 MF8 A 601 " 0.003 2.00e-02 2.50e+03 pdb=" C04 MF8 A 601 " -0.044 2.00e-02 2.50e+03 pdb=" C07 MF8 A 601 " -0.017 2.00e-02 2.50e+03 pdb=" N02 MF8 A 601 " 0.014 2.00e-02 2.50e+03 pdb=" N05 MF8 A 601 " -0.008 2.00e-02 2.50e+03 pdb=" N06 MF8 A 601 " -0.152 2.00e-02 2.50e+03 pdb=" N08 MF8 A 601 " 0.037 2.00e-02 2.50e+03 pdb=" N09 MF8 A 601 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 258 " -0.038 5.00e-02 4.00e+02 5.82e-02 5.43e+00 pdb=" N PRO A 259 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 33 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 34 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 34 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 34 " -0.021 5.00e-02 4.00e+02 ... (remaining 537 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 868 2.81 - 3.34: 3172 3.34 - 3.86: 5115 3.86 - 4.38: 5226 4.38 - 4.90: 9313 Nonbonded interactions: 23694 Sorted by model distance: nonbonded pdb=" OH TYR A 72 " pdb=" O VAL A 103 " model vdw 2.293 2.440 nonbonded pdb=" OG SER A 409 " pdb=" O GLY A 441 " model vdw 2.302 2.440 nonbonded pdb=" OD1 ASN A 186 " pdb=" NE2 GLN A 209 " model vdw 2.341 2.520 nonbonded pdb=" O CYS A 88 " pdb=" NH1 ARG A 89 " model vdw 2.350 2.520 nonbonded pdb=" O ILE A 392 " pdb=" OG1 THR A 396 " model vdw 2.369 2.440 ... (remaining 23689 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.000 Find NCS groups from input model: 0.020 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 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 0.170 3139 Z= 0.352 Angle : 0.664 8.457 4305 Z= 0.366 Chirality : 0.039 0.126 524 Planarity : 0.005 0.067 540 Dihedral : 12.161 65.075 997 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.36 % Allowed : 1.44 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.41), residues: 431 helix: 1.42 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -2.42 (0.51), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 146 HIS 0.003 0.001 HIS A 48 PHE 0.014 0.001 PHE A 159 TYR 0.013 0.001 TYR A 361 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.258 Fit side-chains REVERT: A 35 ILE cc_start: 0.5840 (mm) cc_final: 0.5552 (mm) outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 0.0963 time to fit residues: 6.3132 Evaluate side-chains 36 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 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 51 GLN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3139 Z= 0.223 Angle : 0.610 9.063 4305 Z= 0.302 Chirality : 0.039 0.143 524 Planarity : 0.004 0.043 540 Dihedral : 4.350 39.228 456 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.17 % Allowed : 9.75 % Favored : 88.09 % 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: 0.96 (0.41), residues: 431 helix: 1.51 (0.30), residues: 318 sheet: None (None), residues: 0 loop : -1.95 (0.55), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 429 HIS 0.002 0.001 HIS A 49 PHE 0.015 0.001 PHE A 348 TYR 0.006 0.001 TYR A 199 ARG 0.002 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.272 Fit side-chains REVERT: A 435 MET cc_start: 0.6971 (tpp) cc_final: 0.6703 (tpp) REVERT: A 464 LEU cc_start: 0.2950 (OUTLIER) cc_final: 0.2748 (tm) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 0.0943 time to fit residues: 5.5532 Evaluate side-chains 42 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3139 Z= 0.196 Angle : 0.591 9.185 4305 Z= 0.289 Chirality : 0.038 0.144 524 Planarity : 0.004 0.042 540 Dihedral : 4.297 37.956 456 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.25 % Allowed : 11.55 % Favored : 85.20 % 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: 1.03 (0.41), residues: 431 helix: 1.56 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.96 (0.56), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 429 HIS 0.001 0.000 HIS A 49 PHE 0.010 0.001 PHE A 151 TYR 0.007 0.001 TYR A 361 ARG 0.002 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.303 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 42 average time/residue: 0.0844 time to fit residues: 5.1344 Evaluate side-chains 40 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 406 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3139 Z= 0.202 Angle : 0.598 8.944 4305 Z= 0.290 Chirality : 0.038 0.138 524 Planarity : 0.004 0.039 540 Dihedral : 3.915 15.377 454 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.53 % Allowed : 14.80 % Favored : 82.67 % 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: 1.09 (0.41), residues: 431 helix: 1.61 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.93 (0.57), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 429 HIS 0.002 0.001 HIS A 260 PHE 0.010 0.001 PHE A 151 TYR 0.006 0.001 TYR A 361 ARG 0.001 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.303 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 43 average time/residue: 0.0893 time to fit residues: 5.4279 Evaluate side-chains 42 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 37 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3139 Z= 0.196 Angle : 0.597 8.739 4305 Z= 0.290 Chirality : 0.037 0.137 524 Planarity : 0.004 0.041 540 Dihedral : 3.909 14.512 454 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.25 % Allowed : 16.61 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.41), residues: 431 helix: 1.61 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.95 (0.56), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 429 HIS 0.001 0.000 HIS A 48 PHE 0.018 0.001 PHE A 273 TYR 0.017 0.001 TYR A 127 ARG 0.001 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.283 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 41 average time/residue: 0.0981 time to fit residues: 5.5301 Evaluate side-chains 41 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 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 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3139 Z= 0.219 Angle : 0.614 8.982 4305 Z= 0.298 Chirality : 0.038 0.137 524 Planarity : 0.004 0.038 540 Dihedral : 3.943 15.671 454 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.69 % Allowed : 16.97 % Favored : 78.34 % 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: 1.06 (0.41), residues: 431 helix: 1.58 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.92 (0.56), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 217 HIS 0.002 0.000 HIS A 48 PHE 0.014 0.001 PHE A 273 TYR 0.017 0.001 TYR A 127 ARG 0.001 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 37 time to evaluate : 0.309 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 48 average time/residue: 0.1175 time to fit residues: 7.2544 Evaluate side-chains 46 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.0770 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 25 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3139 Z= 0.181 Angle : 0.598 8.947 4305 Z= 0.286 Chirality : 0.037 0.139 524 Planarity : 0.004 0.037 540 Dihedral : 3.905 15.197 454 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.25 % Allowed : 18.77 % Favored : 77.98 % 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: 1.14 (0.42), residues: 431 helix: 1.69 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -2.05 (0.56), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 429 HIS 0.001 0.000 HIS A 49 PHE 0.013 0.001 PHE A 273 TYR 0.012 0.001 TYR A 127 ARG 0.003 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.281 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 43 average time/residue: 0.1010 time to fit residues: 5.9182 Evaluate side-chains 43 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3139 Z= 0.184 Angle : 0.599 8.553 4305 Z= 0.286 Chirality : 0.037 0.132 524 Planarity : 0.003 0.035 540 Dihedral : 3.879 15.220 454 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.25 % Allowed : 20.22 % Favored : 76.53 % 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: 1.15 (0.41), residues: 431 helix: 1.67 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -2.00 (0.56), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 429 HIS 0.001 0.000 HIS A 48 PHE 0.012 0.001 PHE A 273 TYR 0.012 0.001 TYR A 127 ARG 0.001 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.304 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 43 average time/residue: 0.1029 time to fit residues: 6.1240 Evaluate side-chains 41 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.0010 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3139 Z= 0.173 Angle : 0.595 8.454 4305 Z= 0.281 Chirality : 0.037 0.129 524 Planarity : 0.003 0.035 540 Dihedral : 3.877 15.643 454 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.25 % Allowed : 20.94 % Favored : 75.81 % 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: 1.15 (0.42), residues: 431 helix: 1.73 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -2.18 (0.55), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 429 HIS 0.001 0.000 HIS A 49 PHE 0.011 0.001 PHE A 273 TYR 0.011 0.001 TYR A 127 ARG 0.001 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.293 Fit side-chains REVERT: A 387 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.6917 (tp) outliers start: 9 outliers final: 8 residues processed: 43 average time/residue: 0.0923 time to fit residues: 5.4140 Evaluate side-chains 44 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.0970 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3139 Z= 0.196 Angle : 0.622 8.623 4305 Z= 0.292 Chirality : 0.037 0.132 524 Planarity : 0.003 0.035 540 Dihedral : 3.872 15.264 454 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.25 % Allowed : 21.30 % Favored : 75.45 % 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: 1.18 (0.42), residues: 431 helix: 1.72 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -2.08 (0.55), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 429 HIS 0.001 0.001 HIS A 48 PHE 0.020 0.001 PHE A 273 TYR 0.013 0.001 TYR A 127 ARG 0.001 0.000 ARG A 439 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.350 Fit side-chains REVERT: A 387 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7075 (tp) REVERT: A 440 MET cc_start: 0.6956 (tmm) cc_final: 0.6603 (ttp) outliers start: 9 outliers final: 8 residues processed: 42 average time/residue: 0.1019 time to fit residues: 5.9478 Evaluate side-chains 42 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.0570 chunk 24 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.209944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.186105 restraints weight = 3407.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.188819 restraints weight = 2413.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.190995 restraints weight = 1876.824| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3139 Z= 0.190 Angle : 0.616 8.346 4305 Z= 0.290 Chirality : 0.037 0.128 524 Planarity : 0.003 0.035 540 Dihedral : 3.884 14.801 454 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.61 % Allowed : 20.94 % Favored : 75.45 % 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: 1.20 (0.42), residues: 431 helix: 1.73 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -2.12 (0.56), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 429 HIS 0.001 0.000 HIS A 48 PHE 0.020 0.001 PHE A 273 TYR 0.012 0.001 TYR A 127 ARG 0.001 0.000 ARG A 439 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 910.73 seconds wall clock time: 20 minutes 34.84 seconds (1234.84 seconds total)