Starting phenix.real_space_refine on Wed Mar 5 17:15:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtv_36653/03_2025/8jtv_36653.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtv_36653/03_2025/8jtv_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/cci-nas-00/data/ceres_data/8jtv_36653/03_2025/8jtv_36653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtv_36653/03_2025/8jtv_36653.map" model { file = "/net/cci-nas-00/data/ceres_data/8jtv_36653/03_2025/8jtv_36653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtv_36653/03_2025/8jtv_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. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 2.67, per 1000 atoms: 0.87 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 421.0 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: 0.36 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: 0.90 Time building geometry restraints manager: 1.02 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: 0.00 - 1.69: 4201 1.69 - 3.38: 77 3.38 - 5.07: 14 5.07 - 6.77: 7 6.77 - 8.46: 6 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 3.040 nonbonded pdb=" OG SER A 409 " pdb=" O GLY A 441 " model vdw 2.302 3.040 nonbonded pdb=" OD1 ASN A 186 " pdb=" NE2 GLN A 209 " model vdw 2.341 3.120 nonbonded pdb=" O CYS A 88 " pdb=" NH1 ARG A 89 " model vdw 2.350 3.120 nonbonded pdb=" O ILE A 392 " pdb=" OG1 THR A 396 " model vdw 2.369 3.040 ... (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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.430 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:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.420 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.321 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: 0.1019 time to fit residues: 6.7391 Evaluate side-chains 36 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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: 0.5980 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.0170 chunk 39 optimal weight: 0.6980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 453 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.215985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.193950 restraints weight = 3369.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.197009 restraints weight = 2277.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.199323 restraints weight = 1709.270| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.1168 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= 0.194 Angle : 0.592 8.491 4305 Z= 0.293 Chirality : 0.038 0.136 524 Planarity : 0.004 0.043 540 Dihedral : 4.312 39.074 456 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.89 % Allowed : 8.66 % Favored : 88.45 % 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: 1.06 (0.41), residues: 431 helix: 1.57 (0.30), residues: 319 sheet: None (None), residues: 0 loop : -1.87 (0.55), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 429 HIS 0.002 0.001 HIS A 49 PHE 0.015 0.001 PHE A 348 TYR 0.009 0.001 TYR A 361 ARG 0.003 0.001 ARG A 89 *********************** 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 44 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.305 Fit side-chains REVERT: A 35 ILE cc_start: 0.6156 (mm) cc_final: 0.5941 (mm) REVERT: A 420 MET cc_start: 0.7609 (ttm) cc_final: 0.7353 (tpp) REVERT: A 435 MET cc_start: 0.6947 (tpp) cc_final: 0.6720 (tpp) outliers start: 8 outliers final: 6 residues processed: 42 average time/residue: 0.0888 time to fit residues: 5.2595 Evaluate side-chains 39 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 275 PHE 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 11 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 8 optimal weight: 0.0870 chunk 27 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.232432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.214646 restraints weight = 3227.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.216508 restraints weight = 2444.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.217298 restraints weight = 1983.254| |-----------------------------------------------------------------------------| r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.1522 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= 0.192 Angle : 0.590 8.704 4305 Z= 0.290 Chirality : 0.037 0.134 524 Planarity : 0.004 0.038 540 Dihedral : 4.263 37.611 456 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.25 % Allowed : 10.83 % Favored : 85.92 % 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: 1.61 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.76 (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 0.013 0.001 PHE A 273 TYR 0.009 0.001 TYR A 361 ARG 0.002 0.001 ARG A 89 *********************** 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 to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.333 Fit side-chains REVERT: A 217 TRP cc_start: 0.5990 (t60) cc_final: 0.5787 (t60) REVERT: A 440 MET cc_start: 0.7045 (tmm) cc_final: 0.6615 (ttp) outliers start: 9 outliers final: 6 residues processed: 43 average time/residue: 0.0973 time to fit residues: 5.8631 Evaluate side-chains 41 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 48 HIS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 7 optimal weight: 0.0970 chunk 40 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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 = 0.4650 r_free = 0.4650 target = 0.232636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.214893 restraints weight = 3323.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.216120 restraints weight = 2595.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.216215 restraints weight = 2229.198| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.1728 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= 0.183 Angle : 0.586 8.676 4305 Z= 0.285 Chirality : 0.037 0.138 524 Planarity : 0.004 0.041 540 Dihedral : 3.881 15.269 454 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.53 % Allowed : 15.16 % Favored : 82.31 % 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: 1.22 (0.41), residues: 431 helix: 1.68 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.84 (0.56), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 429 HIS 0.002 0.001 HIS A 49 PHE 0.011 0.001 PHE A 151 TYR 0.009 0.001 TYR A 361 ARG 0.002 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 40 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.299 Fit side-chains REVERT: A 217 TRP cc_start: 0.5979 (t60) cc_final: 0.5760 (t60) outliers start: 7 outliers final: 6 residues processed: 39 average time/residue: 0.1152 time to fit residues: 6.1715 Evaluate side-chains 39 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 7 optimal weight: 0.0270 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.207673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.184838 restraints weight = 3389.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.187495 restraints weight = 2436.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.189226 restraints weight = 1903.976| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.1983 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 : 0.619 8.774 4305 Z= 0.301 Chirality : 0.038 0.136 524 Planarity : 0.004 0.039 540 Dihedral : 3.924 14.099 454 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.89 % Allowed : 16.61 % Favored : 80.51 % 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: 1.13 (0.41), residues: 431 helix: 1.59 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.79 (0.57), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 429 HIS 0.002 0.001 HIS A 49 PHE 0.013 0.001 PHE A 273 TYR 0.007 0.001 TYR A 361 ARG 0.002 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 45 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.306 Fit side-chains REVERT: A 217 TRP cc_start: 0.6137 (t60) cc_final: 0.5907 (t60) REVERT: A 440 MET cc_start: 0.7089 (tmm) cc_final: 0.6565 (ttp) outliers start: 8 outliers final: 7 residues processed: 44 average time/residue: 0.1343 time to fit residues: 7.5542 Evaluate side-chains 42 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 371 THR Chi-restraints excluded: chain A residue 385 VAL 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 20 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4298 r_free = 0.4298 target = 0.209126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.185055 restraints weight = 3494.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.187854 restraints weight = 2460.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.190272 restraints weight = 1904.190| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 0.2153 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= 0.194 Angle : 0.605 8.581 4305 Z= 0.294 Chirality : 0.037 0.138 524 Planarity : 0.004 0.040 540 Dihedral : 3.980 14.614 454 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.33 % Allowed : 16.97 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.41), residues: 431 helix: 1.67 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -1.86 (0.56), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 429 HIS 0.002 0.001 HIS A 49 PHE 0.018 0.001 PHE A 273 TYR 0.008 0.001 TYR A 361 ARG 0.004 0.001 ARG A 462 *********************** 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 45 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.337 Fit side-chains REVERT: A 217 TRP cc_start: 0.5949 (t60) cc_final: 0.5686 (t60) outliers start: 12 outliers final: 9 residues processed: 43 average time/residue: 0.1058 time to fit residues: 6.3025 Evaluate side-chains 42 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 48 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 4 optimal weight: 0.0270 chunk 26 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 = 0.4291 r_free = 0.4291 target = 0.208503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.183960 restraints weight = 3473.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.186845 restraints weight = 2464.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.188530 restraints weight = 1921.560| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.2211 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 : 0.626 8.939 4305 Z= 0.300 Chirality : 0.038 0.140 524 Planarity : 0.004 0.038 540 Dihedral : 3.992 14.813 454 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.61 % Allowed : 18.05 % 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: 1.14 (0.41), residues: 431 helix: 1.64 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.90 (0.55), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 429 HIS 0.002 0.001 HIS A 49 PHE 0.016 0.001 PHE A 273 TYR 0.008 0.001 TYR A 361 ARG 0.001 0.000 ARG A 89 *********************** 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 43 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.286 Fit side-chains REVERT: A 217 TRP cc_start: 0.6030 (t60) cc_final: 0.5752 (t60) REVERT: A 440 MET cc_start: 0.7042 (tmm) cc_final: 0.6414 (ttp) outliers start: 10 outliers final: 9 residues processed: 41 average time/residue: 0.0939 time to fit residues: 5.4258 Evaluate side-chains 40 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 48 HIS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 5 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 22 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 0.0870 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.4307 r_free = 0.4307 target = 0.209851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.185531 restraints weight = 3468.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.188281 restraints weight = 2495.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.189855 restraints weight = 1965.189| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 0.2343 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= 0.194 Angle : 0.622 8.563 4305 Z= 0.296 Chirality : 0.037 0.132 524 Planarity : 0.004 0.037 540 Dihedral : 4.003 15.820 454 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.33 % Allowed : 18.77 % Favored : 76.90 % 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: 1.13 (0.41), residues: 431 helix: 1.65 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.99 (0.54), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 429 HIS 0.002 0.001 HIS A 48 PHE 0.014 0.001 PHE A 273 TYR 0.008 0.001 TYR A 361 ARG 0.002 0.000 ARG A 462 *********************** 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 44 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.291 Fit side-chains REVERT: A 217 TRP cc_start: 0.6027 (t60) cc_final: 0.5758 (t60) REVERT: A 387 ILE cc_start: 0.6866 (OUTLIER) cc_final: 0.6549 (tp) REVERT: A 440 MET cc_start: 0.7180 (tmm) cc_final: 0.6588 (ttp) outliers start: 12 outliers final: 9 residues processed: 42 average time/residue: 0.0867 time to fit residues: 5.1692 Evaluate side-chains 42 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 48 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 37 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 0.0470 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.4308 r_free = 0.4308 target = 0.210210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.185549 restraints weight = 3492.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.188330 restraints weight = 2490.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.189528 restraints weight = 1940.407| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.2331 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= 0.191 Angle : 0.617 8.489 4305 Z= 0.293 Chirality : 0.037 0.132 524 Planarity : 0.004 0.037 540 Dihedral : 3.982 15.430 454 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.97 % Allowed : 19.49 % 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: 1.19 (0.41), residues: 431 helix: 1.68 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -1.94 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 429 HIS 0.002 0.001 HIS A 49 PHE 0.014 0.001 PHE A 273 TYR 0.008 0.001 TYR A 361 ARG 0.001 0.000 ARG A 462 *********************** 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 to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.296 Fit side-chains REVERT: A 217 TRP cc_start: 0.6119 (t60) cc_final: 0.5845 (t60) REVERT: A 387 ILE cc_start: 0.6834 (OUTLIER) cc_final: 0.6503 (tp) outliers start: 11 outliers final: 9 residues processed: 42 average time/residue: 0.0993 time to fit residues: 5.7234 Evaluate side-chains 42 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 48 HIS 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 36 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4287 r_free = 0.4287 target = 0.207555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.182956 restraints weight = 3458.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.185601 restraints weight = 2496.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.187686 restraints weight = 1970.942| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.2518 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= 0.220 Angle : 0.655 8.601 4305 Z= 0.310 Chirality : 0.038 0.136 524 Planarity : 0.004 0.037 540 Dihedral : 4.040 15.207 454 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.61 % Allowed : 20.22 % Favored : 76.17 % 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: 1.11 (0.41), residues: 431 helix: 1.60 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -1.91 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 429 HIS 0.002 0.001 HIS A 48 PHE 0.021 0.001 PHE A 273 TYR 0.007 0.001 TYR A 361 ARG 0.002 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 44 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.323 Fit side-chains REVERT: A 217 TRP cc_start: 0.6156 (t60) cc_final: 0.5866 (t60) REVERT: A 387 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.6644 (tp) outliers start: 10 outliers final: 9 residues processed: 43 average time/residue: 0.1043 time to fit residues: 6.2081 Evaluate side-chains 43 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 48 HIS 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: 0.8980 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.0770 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.4318 r_free = 0.4318 target = 0.211435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.186566 restraints weight = 3495.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.189680 restraints weight = 2485.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.191301 restraints weight = 1932.345| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 moved from start: 0.2465 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= 0.183 Angle : 0.633 10.257 4305 Z= 0.298 Chirality : 0.037 0.128 524 Planarity : 0.004 0.063 540 Dihedral : 3.981 14.818 454 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.61 % Allowed : 20.22 % Favored : 76.17 % 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: 1.17 (0.41), residues: 431 helix: 1.67 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -2.01 (0.54), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 429 HIS 0.001 0.001 HIS A 49 PHE 0.020 0.001 PHE A 273 TYR 0.008 0.001 TYR A 361 ARG 0.002 0.000 ARG A 462 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1213.72 seconds wall clock time: 21 minutes 40.30 seconds (1300.30 seconds total)