Starting phenix.real_space_refine on Wed Sep 17 03:52:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j2n_61099/09_2025/9j2n_61099.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j2n_61099/09_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_61099/09_2025/9j2n_61099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j2n_61099/09_2025/9j2n_61099.map" model { file = "/net/cci-nas-00/data/ceres_data/9j2n_61099/09_2025/9j2n_61099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j2n_61099/09_2025/9j2n_61099.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU: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: 1.16, per 1000 atoms: 0.32 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: 0.30 Conformation dependent library (CDL) restraints added in 145.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.09 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: 0.59 Time building geometry restraints manager: 0.40 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: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.400 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.370 ------------------------------------------------------------------------------- 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= 0.376 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 414 TYR 0.017 0.002 TYR A 60 PHE 0.018 0.001 PHE A 36 TRP 0.007 0.001 TRP A 77 HIS 0.002 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00560 ( 3661) covalent geometry : angle 0.80997 ( 4982) hydrogen bonds : bond 0.14772 ( 272) hydrogen bonds : angle 6.22577 ( 816) *********************** 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 : 0.187 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0831 time to fit residues: 7.8304 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 : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 0.0170 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.159198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127256 restraints weight = 4525.213| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.03 r_work: 0.3308 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3661 Z= 0.142 Angle : 0.610 8.541 4982 Z= 0.310 Chirality : 0.040 0.177 601 Planarity : 0.005 0.070 618 Dihedral : 8.304 57.389 531 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.32 % Allowed : 16.40 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.39), residues: 466 helix: 1.33 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -1.95 (0.61), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 257 TYR 0.008 0.001 TYR A 310 PHE 0.011 0.001 PHE A 175 TRP 0.008 0.001 TRP A 77 HIS 0.003 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 3661) covalent geometry : angle 0.61050 ( 4982) hydrogen bonds : bond 0.04453 ( 272) hydrogen bonds : angle 4.84270 ( 816) *********************** 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 71 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.130 Fit side-chains REVERT: A 189 GLN cc_start: 0.8425 (tp40) cc_final: 0.8171 (tp-100) REVERT: A 232 ASP cc_start: 0.8064 (t70) cc_final: 0.7461 (t70) outliers start: 5 outliers final: 3 residues processed: 70 average time/residue: 0.0717 time to fit residues: 6.1877 Evaluate side-chains 63 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 384 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 41 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS A 163 ASN A 411 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.159807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.127417 restraints weight = 4409.254| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.97 r_work: 0.3284 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1882 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= 0.135 Angle : 0.546 6.484 4982 Z= 0.285 Chirality : 0.038 0.137 601 Planarity : 0.005 0.072 618 Dihedral : 5.217 50.170 531 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.59 % Allowed : 16.93 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.39), residues: 466 helix: 1.39 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -2.05 (0.61), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 244 TYR 0.017 0.001 TYR A 304 PHE 0.014 0.001 PHE A 436 TRP 0.008 0.001 TRP A 77 HIS 0.003 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3661) covalent geometry : angle 0.54633 ( 4982) hydrogen bonds : bond 0.04070 ( 272) hydrogen bonds : angle 4.61247 ( 816) *********************** 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 69 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.132 Fit side-chains REVERT: A 73 MET cc_start: 0.7983 (tpp) cc_final: 0.7682 (tpp) REVERT: A 99 VAL cc_start: 0.8791 (p) cc_final: 0.8540 (m) REVERT: A 189 GLN cc_start: 0.8428 (tp40) cc_final: 0.8158 (tp-100) REVERT: A 434 PHE cc_start: 0.7793 (t80) cc_final: 0.7526 (t80) outliers start: 6 outliers final: 5 residues processed: 68 average time/residue: 0.0682 time to fit residues: 5.8119 Evaluate side-chains 64 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 191 ILE 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 6 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.156745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124598 restraints weight = 4438.459| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.94 r_work: 0.3218 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3661 Z= 0.164 Angle : 0.554 6.382 4982 Z= 0.291 Chirality : 0.039 0.136 601 Planarity : 0.005 0.076 618 Dihedral : 5.422 58.700 531 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.65 % Allowed : 16.40 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.39), residues: 466 helix: 1.45 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -2.05 (0.60), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 104 TYR 0.017 0.001 TYR A 304 PHE 0.014 0.001 PHE A 436 TRP 0.008 0.002 TRP A 77 HIS 0.004 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 3661) covalent geometry : angle 0.55441 ( 4982) hydrogen bonds : bond 0.04292 ( 272) hydrogen bonds : angle 4.63279 ( 816) *********************** 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 69 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: A 99 VAL cc_start: 0.8837 (p) cc_final: 0.8570 (m) REVERT: A 189 GLN cc_start: 0.8524 (tp40) cc_final: 0.8246 (tp-100) outliers start: 10 outliers final: 7 residues processed: 67 average time/residue: 0.0676 time to fit residues: 5.7236 Evaluate side-chains 64 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 42 optimal weight: 0.0040 chunk 45 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.159138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.126080 restraints weight = 4398.320| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.02 r_work: 0.3281 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2291 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= 0.129 Angle : 0.535 8.990 4982 Z= 0.278 Chirality : 0.038 0.142 601 Planarity : 0.005 0.075 618 Dihedral : 4.812 42.159 531 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.85 % Allowed : 17.99 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.39), residues: 466 helix: 1.51 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -2.09 (0.59), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 241 TYR 0.018 0.001 TYR A 304 PHE 0.036 0.001 PHE A 434 TRP 0.008 0.001 TRP A 77 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 3661) covalent geometry : angle 0.53548 ( 4982) hydrogen bonds : bond 0.03898 ( 272) hydrogen bonds : angle 4.51367 ( 816) *********************** 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 66 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 99 VAL cc_start: 0.8813 (p) cc_final: 0.8568 (m) REVERT: A 189 GLN cc_start: 0.8511 (tp40) cc_final: 0.8225 (tp-100) REVERT: A 434 PHE cc_start: 0.7733 (t80) cc_final: 0.7512 (t80) REVERT: A 440 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8102 (tm-30) outliers start: 7 outliers final: 6 residues processed: 63 average time/residue: 0.0662 time to fit residues: 5.2390 Evaluate side-chains 61 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 373 ASN Chi-restraints excluded: chain A residue 384 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 0.0980 chunk 40 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 0.0170 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN A 393 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.162342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.130022 restraints weight = 4299.418| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.92 r_work: 0.3319 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2467 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= 0.116 Angle : 0.507 6.361 4982 Z= 0.265 Chirality : 0.037 0.139 601 Planarity : 0.005 0.074 618 Dihedral : 4.100 16.739 531 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.85 % Allowed : 17.99 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.39), residues: 466 helix: 1.53 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -2.08 (0.61), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 241 TYR 0.007 0.001 TYR A 40 PHE 0.026 0.001 PHE A 434 TRP 0.008 0.001 TRP A 77 HIS 0.002 0.000 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3661) covalent geometry : angle 0.50684 ( 4982) hydrogen bonds : bond 0.03474 ( 272) hydrogen bonds : angle 4.38243 ( 816) *********************** 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 70 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 99 VAL cc_start: 0.8701 (p) cc_final: 0.8489 (m) REVERT: A 434 PHE cc_start: 0.7649 (t80) cc_final: 0.7374 (t80) REVERT: A 435 LEU cc_start: 0.8248 (tp) cc_final: 0.8037 (tp) outliers start: 7 outliers final: 4 residues processed: 69 average time/residue: 0.0779 time to fit residues: 6.5747 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 : 0.134 ------------------------------------------------------------------------------- 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 300 ASN Chi-restraints excluded: chain A residue 342 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.160446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.128453 restraints weight = 4417.475| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.91 r_work: 0.3293 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2532 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= 0.132 Angle : 0.534 6.709 4982 Z= 0.277 Chirality : 0.038 0.138 601 Planarity : 0.005 0.073 618 Dihedral : 4.017 16.582 531 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.85 % Allowed : 18.52 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.39), residues: 466 helix: 1.55 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -2.06 (0.60), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 241 TYR 0.007 0.001 TYR A 60 PHE 0.021 0.001 PHE A 434 TRP 0.007 0.001 TRP A 77 HIS 0.003 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3661) covalent geometry : angle 0.53416 ( 4982) hydrogen bonds : bond 0.03728 ( 272) hydrogen bonds : angle 4.40918 ( 816) *********************** 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: 7 poor density : 56 time to evaluate : 0.083 Fit side-chains REVERT: A 435 LEU cc_start: 0.8250 (tp) cc_final: 0.8049 (tp) outliers start: 7 outliers final: 6 residues processed: 61 average time/residue: 0.0674 time to fit residues: 5.1029 Evaluate side-chains 61 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.105 ------------------------------------------------------------------------------- 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 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 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.160927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128151 restraints weight = 4392.156| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.94 r_work: 0.3294 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3661 Z= 0.127 Angle : 0.530 7.125 4982 Z= 0.275 Chirality : 0.038 0.139 601 Planarity : 0.005 0.074 618 Dihedral : 3.956 16.476 531 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.59 % Allowed : 19.84 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.39), residues: 466 helix: 1.55 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -2.06 (0.61), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 241 TYR 0.007 0.001 TYR A 60 PHE 0.013 0.001 PHE A 436 TRP 0.008 0.001 TRP A 77 HIS 0.002 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3661) covalent geometry : angle 0.53003 ( 4982) hydrogen bonds : bond 0.03662 ( 272) hydrogen bonds : angle 4.37514 ( 816) *********************** 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 63 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.143 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 61 average time/residue: 0.0843 time to fit residues: 6.2552 Evaluate side-chains 60 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 300 ASN Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 363 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.159953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.127084 restraints weight = 4415.261| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.94 r_work: 0.3298 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2684 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= 0.136 Angle : 0.546 7.557 4982 Z= 0.282 Chirality : 0.038 0.137 601 Planarity : 0.005 0.075 618 Dihedral : 4.000 16.432 531 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.85 % Allowed : 20.11 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.39), residues: 466 helix: 1.60 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -2.11 (0.59), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 241 TYR 0.007 0.001 TYR A 60 PHE 0.013 0.001 PHE A 436 TRP 0.008 0.001 TRP A 77 HIS 0.003 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3661) covalent geometry : angle 0.54592 ( 4982) hydrogen bonds : bond 0.03774 ( 272) hydrogen bonds : angle 4.39372 ( 816) *********************** 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 60 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.096 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 57 average time/residue: 0.0704 time to fit residues: 4.9734 Evaluate side-chains 59 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.134 ------------------------------------------------------------------------------- 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 300 ASN Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 384 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 0.0980 chunk 40 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.153638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121457 restraints weight = 4396.473| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.91 r_work: 0.3292 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2769 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= 0.125 Angle : 0.539 7.688 4982 Z= 0.277 Chirality : 0.038 0.133 601 Planarity : 0.005 0.076 618 Dihedral : 3.962 16.451 531 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.32 % Allowed : 20.63 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.39), residues: 466 helix: 1.65 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -2.15 (0.59), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 241 TYR 0.007 0.001 TYR A 40 PHE 0.013 0.001 PHE A 436 TRP 0.008 0.001 TRP A 77 HIS 0.002 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 3661) covalent geometry : angle 0.53932 ( 4982) hydrogen bonds : bond 0.03601 ( 272) hydrogen bonds : angle 4.33917 ( 816) ********************** 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 61 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.131 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 59 average time/residue: 0.0703 time to fit residues: 5.1829 Evaluate side-chains 59 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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 300 ASN Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 363 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 0.0050 chunk 18 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.153835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121654 restraints weight = 4328.125| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.90 r_work: 0.3300 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2806 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= 0.121 Angle : 0.537 7.809 4982 Z= 0.276 Chirality : 0.037 0.131 601 Planarity : 0.005 0.076 618 Dihedral : 3.970 16.206 531 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.32 % Allowed : 20.63 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.39), residues: 466 helix: 1.57 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -2.12 (0.60), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 241 TYR 0.007 0.001 TYR A 60 PHE 0.013 0.001 PHE A 436 TRP 0.008 0.001 TRP A 77 HIS 0.003 0.001 HIS A 393 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3661) covalent geometry : angle 0.53743 ( 4982) hydrogen bonds : bond 0.03534 ( 272) hydrogen bonds : angle 4.34924 ( 816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1089.73 seconds wall clock time: 19 minutes 22.95 seconds (1162.95 seconds total)