Starting phenix.real_space_refine on Mon Jan 13 18:15:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j2n_61099/01_2025/9j2n_61099.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j2n_61099/01_2025/9j2n_61099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j2n_61099/01_2025/9j2n_61099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j2n_61099/01_2025/9j2n_61099.map" model { file = "/net/cci-nas-00/data/ceres_data/9j2n_61099/01_2025/9j2n_61099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j2n_61099/01_2025/9j2n_61099.cif" } resolution = 3.3 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= 0.015 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 20 5.16 5 C 2342 2.51 5 N 596 2.21 5 O 626 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-5571/modules/chem_data/mon_lib" Total number of atoms: 3584 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3569 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 18, 'TRANS': 449} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.95, per 1000 atoms: 0.82 Number of scatterers: 3584 At special positions: 0 Unit cell: (86.1, 55.678, 67.732, 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 20 16.00 O 626 8.00 N 596 7.00 C 2342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 438.1 milliseconds 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 858 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 86.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 20 through 43 removed outlier: 3.577A pdb=" N GLY A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLN A 37 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 65 removed outlier: 3.651A pdb=" N PHE A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 93 removed outlier: 5.234A pdb=" N PHE A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) Proline residue: A 85 - end of helix Processing helix chain 'A' and resid 94 through 112 removed outlier: 4.031A pdb=" N ASP A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ARG A 104 " --> pdb=" O ASP A 100 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N LYS A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 124 Proline residue: A 118 - end of helix Processing helix chain 'A' and resid 131 through 160 removed outlier: 3.538A pdb=" N ARG A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 164 through 187 removed outlier: 3.530A pdb=" N VAL A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 222 through 229 Processing helix chain 'A' and resid 232 through 244 Processing helix chain 'A' and resid 249 through 267 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 298 through 313 removed outlier: 4.457A pdb=" N ASP A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR A 308 " --> pdb=" O TYR A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 346 removed outlier: 3.569A pdb=" N THR A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG A 344 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 371 removed outlier: 3.866A pdb=" N LEU A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 378 through 396 Processing helix chain 'A' and resid 398 through 408 removed outlier: 4.212A pdb=" N SER A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 434 Processing helix chain 'A' and resid 435 through 444 Processing helix chain 'A' and resid 446 through 465 Processing helix chain 'A' and resid 473 through 485 removed outlier: 3.669A pdb=" N ASN A 485 " --> pdb=" O PHE A 481 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 880 1.33 - 1.45: 754 1.45 - 1.57: 1995 1.57 - 1.70: 0 1.70 - 1.82: 32 Bond restraints: 3661 Sorted by residual: bond pdb=" CA LEU A 90 " pdb=" C LEU A 90 " ideal model delta sigma weight residual 1.524 1.488 0.035 1.29e-02 6.01e+03 7.46e+00 bond pdb=" CA GLN A 440 " pdb=" C GLN A 440 " ideal model delta sigma weight residual 1.523 1.488 0.035 1.35e-02 5.49e+03 6.79e+00 bond pdb=" CA GLN A 294 " pdb=" C GLN A 294 " ideal model delta sigma weight residual 1.524 1.490 0.034 1.37e-02 5.33e+03 6.10e+00 bond pdb=" C1 NAG A 601 " pdb=" O1 NAG A 601 " ideal model delta sigma weight residual 1.376 1.425 -0.049 2.00e-02 2.50e+03 5.99e+00 bond pdb=" CA ALA A 236 " pdb=" C ALA A 236 " ideal model delta sigma weight residual 1.523 1.493 0.030 1.30e-02 5.92e+03 5.47e+00 ... (remaining 3656 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 4888 2.63 - 5.25: 83 5.25 - 7.88: 8 7.88 - 10.50: 1 10.50 - 13.13: 2 Bond angle restraints: 4982 Sorted by residual: angle pdb=" C THR A 247 " pdb=" CA THR A 247 " pdb=" CB THR A 247 " ideal model delta sigma weight residual 116.54 109.52 7.02 1.15e+00 7.56e-01 3.73e+01 angle pdb=" N TYR A 446 " pdb=" CA TYR A 446 " pdb=" C TYR A 446 " ideal model delta sigma weight residual 113.20 106.54 6.66 1.21e+00 6.83e-01 3.03e+01 angle pdb=" C PHE A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 119.24 113.81 5.43 1.04e+00 9.25e-01 2.73e+01 angle pdb=" N GLY A 298 " pdb=" CA GLY A 298 " pdb=" C GLY A 298 " ideal model delta sigma weight residual 114.64 121.58 -6.94 1.40e+00 5.10e-01 2.46e+01 angle pdb=" N SER A 447 " pdb=" CA SER A 447 " pdb=" C SER A 447 " ideal model delta sigma weight residual 111.28 106.11 5.17 1.09e+00 8.42e-01 2.25e+01 ... (remaining 4977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.19: 1973 20.19 - 40.38: 153 40.38 - 60.57: 24 60.57 - 80.76: 4 80.76 - 100.94: 11 Dihedral angle restraints: 2165 sinusoidal: 823 harmonic: 1342 Sorted by residual: dihedral pdb=" C5 NAG A 601 " pdb=" C3 NAG A 601 " pdb=" C4 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sinusoidal sigma weight residual -174.13 -73.19 -100.94 1 3.00e+01 1.11e-03 1.27e+01 dihedral pdb=" C2 NAG A 601 " pdb=" C3 NAG A 601 " pdb=" C4 NAG A 601 " pdb=" C5 NAG A 601 " ideal model delta sinusoidal sigma weight residual 53.78 -46.50 100.28 1 3.00e+01 1.11e-03 1.26e+01 dihedral pdb=" O3 NAG A 601 " pdb=" C3 NAG A 601 " pdb=" C4 NAG A 601 " pdb=" O4 NAG A 601 " ideal model delta sinusoidal sigma weight residual -64.55 -163.60 99.05 1 3.00e+01 1.11e-03 1.23e+01 ... (remaining 2162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 367 0.029 - 0.059: 148 0.059 - 0.088: 55 0.088 - 0.117: 27 0.117 - 0.147: 4 Chirality restraints: 601 Sorted by residual: chirality pdb=" CA GLN A 229 " pdb=" N GLN A 229 " pdb=" C GLN A 229 " pdb=" CB GLN A 229 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA PHE A 448 " pdb=" N PHE A 448 " pdb=" C PHE A 448 " pdb=" CB PHE A 448 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA THR A 47 " pdb=" N THR A 47 " pdb=" C THR A 47 " pdb=" CB THR A 47 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 598 not shown) Planarity restraints: 618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " 0.345 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG A 601 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " -0.518 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " 0.212 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 396 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO A 397 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 397 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 397 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 432 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C ILE A 432 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE A 432 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY A 433 " -0.012 2.00e-02 2.50e+03 ... (remaining 615 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 776 2.77 - 3.30: 3760 3.30 - 3.83: 6165 3.83 - 4.37: 7139 4.37 - 4.90: 12279 Nonbonded interactions: 30119 Sorted by model distance: nonbonded pdb=" NE1 TRP A 282 " pdb=" OD1 ASN A 485 " model vdw 2.233 3.120 nonbonded pdb=" ND2 ASN A 112 " pdb=" OE1 GLN A 212 " model vdw 2.249 3.120 nonbonded pdb=" O SER A 297 " pdb=" OH TYR A 389 " model vdw 2.276 3.040 nonbonded pdb=" O GLN A 189 " pdb=" NE2 GLN A 189 " model vdw 2.287 3.120 nonbonded pdb=" OE2 GLU A 263 " pdb=" N SER A 412 " model vdw 2.318 3.120 ... (remaining 30114 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.160 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.290 Find NCS groups from input model: 0.040 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 0.049 3661 Z= 0.363 Angle : 0.810 13.130 4982 Z= 0.512 Chirality : 0.040 0.147 601 Planarity : 0.013 0.297 618 Dihedral : 16.618 100.944 1307 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 15.34 % Favored : 84.66 % 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: 0.45 (0.38), residues: 466 helix: 0.92 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -1.86 (0.58), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 77 HIS 0.002 0.001 HIS A 64 PHE 0.018 0.001 PHE A 36 TYR 0.017 0.002 TYR A 60 ARG 0.002 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.390 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1925 time to fit residues: 18.3854 Evaluate side-chains 61 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 64 HIS A 112 ASN A 163 ASN A 212 GLN A 300 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.158359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126984 restraints weight = 4400.640| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.95 r_work: 0.3275 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3661 Z= 0.210 Angle : 0.614 8.168 4982 Z= 0.313 Chirality : 0.040 0.166 601 Planarity : 0.005 0.070 618 Dihedral : 8.146 55.567 531 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.85 % Allowed : 15.61 % Favored : 82.54 % 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: 0.97 (0.39), residues: 466 helix: 1.30 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -1.98 (0.61), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 77 HIS 0.003 0.001 HIS A 425 PHE 0.012 0.001 PHE A 175 TYR 0.008 0.001 TYR A 310 ARG 0.002 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 189 GLN cc_start: 0.8454 (tp40) cc_final: 0.8214 (tp-100) REVERT: A 232 ASP cc_start: 0.8121 (t70) cc_final: 0.7546 (t70) outliers start: 7 outliers final: 4 residues processed: 72 average time/residue: 0.1775 time to fit residues: 16.0603 Evaluate side-chains 65 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 384 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS A 112 ASN A 163 ASN A 212 GLN A 411 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.157086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124918 restraints weight = 4347.663| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.93 r_work: 0.3248 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3661 Z= 0.231 Angle : 0.564 6.504 4982 Z= 0.294 Chirality : 0.039 0.135 601 Planarity : 0.005 0.075 618 Dihedral : 5.404 55.501 531 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.38 % Allowed : 16.40 % Favored : 81.22 % 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 (0.39), residues: 466 helix: 1.41 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -2.08 (0.59), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 77 HIS 0.003 0.001 HIS A 425 PHE 0.014 0.001 PHE A 436 TYR 0.016 0.001 TYR A 304 ARG 0.002 0.000 ARG A 244 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.8047 (tpp) cc_final: 0.7828 (tpp) REVERT: A 99 VAL cc_start: 0.8834 (p) cc_final: 0.8612 (m) REVERT: A 189 GLN cc_start: 0.8487 (tp40) cc_final: 0.8221 (tp-100) REVERT: A 434 PHE cc_start: 0.7864 (t80) cc_final: 0.7655 (t80) outliers start: 9 outliers final: 7 residues processed: 70 average time/residue: 0.1547 time to fit residues: 13.7632 Evaluate side-chains 68 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 373 ASN Chi-restraints excluded: chain A residue 384 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 42 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 0 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.160121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.128357 restraints weight = 4416.786| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.93 r_work: 0.3297 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3661 Z= 0.176 Angle : 0.520 6.371 4982 Z= 0.273 Chirality : 0.038 0.137 601 Planarity : 0.005 0.074 618 Dihedral : 5.187 52.822 531 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.85 % Allowed : 16.93 % Favored : 81.22 % 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: 1.16 (0.39), residues: 466 helix: 1.41 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -2.00 (0.61), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 77 HIS 0.002 0.001 HIS A 425 PHE 0.013 0.001 PHE A 436 TYR 0.016 0.001 TYR A 304 ARG 0.002 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 99 VAL cc_start: 0.8817 (p) cc_final: 0.8600 (m) REVERT: A 189 GLN cc_start: 0.8476 (tp40) cc_final: 0.8218 (tp-100) outliers start: 7 outliers final: 4 residues processed: 69 average time/residue: 0.1493 time to fit residues: 13.0494 Evaluate side-chains 66 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 373 ASN Chi-restraints excluded: chain A residue 384 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS A 112 ASN A 212 GLN A 295 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.160700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.128840 restraints weight = 4415.808| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.92 r_work: 0.3322 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3661 Z= 0.177 Angle : 0.529 8.950 4982 Z= 0.275 Chirality : 0.038 0.132 601 Planarity : 0.005 0.073 618 Dihedral : 4.529 33.581 531 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.32 % Allowed : 19.31 % Favored : 79.37 % 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 (0.39), residues: 466 helix: 1.48 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -2.06 (0.61), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 77 HIS 0.003 0.001 HIS A 64 PHE 0.034 0.001 PHE A 434 TYR 0.018 0.001 TYR A 304 ARG 0.003 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 99 VAL cc_start: 0.8789 (p) cc_final: 0.8559 (m) REVERT: A 434 PHE cc_start: 0.7753 (t80) cc_final: 0.7527 (t80) outliers start: 5 outliers final: 3 residues processed: 66 average time/residue: 0.1612 time to fit residues: 13.2553 Evaluate side-chains 59 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 363 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 35 optimal weight: 0.0050 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.161559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.129267 restraints weight = 4386.889| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.92 r_work: 0.3322 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3661 Z= 0.173 Angle : 0.523 6.368 4982 Z= 0.273 Chirality : 0.038 0.133 601 Planarity : 0.005 0.073 618 Dihedral : 4.133 17.041 531 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.85 % Allowed : 17.46 % Favored : 80.69 % 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: 1.31 (0.39), residues: 466 helix: 1.54 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -2.06 (0.61), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 77 HIS 0.002 0.001 HIS A 425 PHE 0.025 0.001 PHE A 434 TYR 0.022 0.001 TYR A 304 ARG 0.003 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 99 VAL cc_start: 0.8763 (p) cc_final: 0.8541 (m) REVERT: A 435 LEU cc_start: 0.8219 (tp) cc_final: 0.7994 (tp) outliers start: 7 outliers final: 4 residues processed: 65 average time/residue: 0.1608 time to fit residues: 12.9727 Evaluate side-chains 61 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 384 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.0000 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.160924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128249 restraints weight = 4363.825| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.98 r_work: 0.3296 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3661 Z= 0.179 Angle : 0.532 6.832 4982 Z= 0.277 Chirality : 0.038 0.135 601 Planarity : 0.005 0.074 618 Dihedral : 4.005 15.801 531 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.06 % Allowed : 19.84 % Favored : 79.10 % 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: 1.35 (0.39), residues: 466 helix: 1.57 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -2.08 (0.60), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 77 HIS 0.002 0.001 HIS A 425 PHE 0.012 0.001 PHE A 436 TYR 0.007 0.001 TYR A 60 ARG 0.009 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.437 Fit side-chains REVERT: A 99 VAL cc_start: 0.8730 (p) cc_final: 0.8511 (m) outliers start: 4 outliers final: 4 residues processed: 61 average time/residue: 0.1809 time to fit residues: 13.6115 Evaluate side-chains 60 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 363 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 16 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 10 optimal weight: 0.0470 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 17 optimal weight: 0.0970 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 overall best weight: 0.3876 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.159603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126375 restraints weight = 4401.946| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.01 r_work: 0.3323 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3661 Z= 0.158 Angle : 0.525 7.008 4982 Z= 0.271 Chirality : 0.037 0.135 601 Planarity : 0.005 0.073 618 Dihedral : 3.941 15.810 531 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.79 % Allowed : 19.84 % Favored : 79.37 % 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: 1.47 (0.39), residues: 466 helix: 1.71 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -2.14 (0.59), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 77 HIS 0.002 0.000 HIS A 425 PHE 0.011 0.001 PHE A 36 TYR 0.007 0.001 TYR A 40 ARG 0.006 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.371 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 61 average time/residue: 0.1602 time to fit residues: 12.1976 Evaluate side-chains 56 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 342 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.152880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120666 restraints weight = 4299.581| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.89 r_work: 0.3295 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3661 Z= 0.205 Angle : 0.558 7.476 4982 Z= 0.285 Chirality : 0.039 0.212 601 Planarity : 0.005 0.073 618 Dihedral : 3.962 15.898 531 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.53 % Allowed : 19.58 % Favored : 79.89 % 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: 1.33 (0.39), residues: 466 helix: 1.56 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -2.06 (0.59), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 77 HIS 0.003 0.001 HIS A 425 PHE 0.013 0.001 PHE A 436 TYR 0.007 0.001 TYR A 60 ARG 0.008 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.393 Fit side-chains REVERT: A 189 GLN cc_start: 0.8375 (tp40) cc_final: 0.8151 (tp-100) outliers start: 2 outliers final: 2 residues processed: 56 average time/residue: 0.1660 time to fit residues: 11.5997 Evaluate side-chains 54 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.0050 chunk 36 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 0.0470 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.5292 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.165355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132937 restraints weight = 4322.326| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.94 r_work: 0.3381 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3661 Z= 0.169 Angle : 0.546 7.736 4982 Z= 0.279 Chirality : 0.038 0.134 601 Planarity : 0.005 0.074 618 Dihedral : 3.962 15.821 531 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.53 % Allowed : 20.37 % Favored : 79.10 % 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: 1.38 (0.39), residues: 466 helix: 1.59 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -2.03 (0.59), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 77 HIS 0.002 0.001 HIS A 425 PHE 0.012 0.001 PHE A 436 TYR 0.007 0.001 TYR A 40 ARG 0.007 0.000 ARG A 241 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.426 Fit side-chains REVERT: A 189 GLN cc_start: 0.8330 (tp40) cc_final: 0.8092 (tp-100) outliers start: 2 outliers final: 2 residues processed: 58 average time/residue: 0.1658 time to fit residues: 12.0452 Evaluate side-chains 56 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.163561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.131182 restraints weight = 4373.120| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.93 r_work: 0.3360 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3661 Z= 0.193 Angle : 0.551 7.812 4982 Z= 0.283 Chirality : 0.038 0.142 601 Planarity : 0.005 0.075 618 Dihedral : 3.973 15.973 531 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.06 % Allowed : 20.11 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.39), residues: 466 helix: 1.56 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -2.02 (0.59), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 77 HIS 0.003 0.001 HIS A 425 PHE 0.013 0.001 PHE A 436 TYR 0.007 0.001 TYR A 60 ARG 0.007 0.000 ARG A 241 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2170.75 seconds wall clock time: 39 minutes 13.07 seconds (2353.07 seconds total)