Starting phenix.real_space_refine on Fri Aug 22 14:49:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ynj_33963/08_2025/7ynj_33963.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ynj_33963/08_2025/7ynj_33963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ynj_33963/08_2025/7ynj_33963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ynj_33963/08_2025/7ynj_33963.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ynj_33963/08_2025/7ynj_33963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ynj_33963/08_2025/7ynj_33963.map" } resolution = 3.33 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= 0.003 sd= 0.075 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 33 5.16 5 C 2905 2.51 5 N 712 2.21 5 O 721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4371 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4145 Classifications: {'peptide': 564} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 26, 'TRANS': 537} Chain breaks: 3 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ARG:plan': 8, 'ASN:plan1': 3, 'ASP:plan': 10, 'GLU:plan': 8, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 121 Chain: "B" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 26} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'GYP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.19, per 1000 atoms: 0.27 Number of scatterers: 4371 At special positions: 0 Unit cell: (74.711, 64.859, 88.668, 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 33 16.00 O 721 8.00 N 712 7.00 C 2905 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 159.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1078 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 81.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 26 through 46 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 112 removed outlier: 4.023A pdb=" N GLU A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE A 104 " --> pdb=" O TRP A 100 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 120 removed outlier: 4.266A pdb=" N VAL A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.723A pdb=" N TYR A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 129 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 152 removed outlier: 4.314A pdb=" N ARG A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 171 Processing helix chain 'A' and resid 173 through 192 Processing helix chain 'A' and resid 200 through 224 removed outlier: 3.630A pdb=" N HIS A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 275 through 281 Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.937A pdb=" N ILE A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.590A pdb=" N VAL A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 removed outlier: 3.957A pdb=" N THR A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 removed outlier: 4.309A pdb=" N MET A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Proline residue: A 331 - end of helix Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'A' and resid 380 through 406 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 418 through 446 Proline residue: A 442 - end of helix removed outlier: 4.149A pdb=" N ALA A 446 " --> pdb=" O PRO A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 450 Processing helix chain 'A' and resid 451 through 477 removed outlier: 3.514A pdb=" N TYR A 455 " --> pdb=" O GLN A 451 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 481 through 507 removed outlier: 3.686A pdb=" N GLY A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Proline residue: A 502 - end of helix Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'A' and resid 525 through 547 Processing helix chain 'A' and resid 552 through 556 Processing helix chain 'A' and resid 560 through 564 removed outlier: 4.050A pdb=" N ARG A 564 " --> pdb=" O PHE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 671 Processing helix chain 'B' and resid 29 through 55 320 hydrogen bonds defined for protein. 948 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: 0.53 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1318 1.34 - 1.46: 1174 1.46 - 1.58: 1950 1.58 - 1.70: 0 1.70 - 1.82: 49 Bond restraints: 4491 Sorted by residual: bond pdb=" C1 GYP A 701 " pdb=" O1 GYP A 701 " ideal model delta sigma weight residual 1.387 1.426 -0.039 2.00e-02 2.50e+03 3.90e+00 bond pdb=" C TYR A 366 " pdb=" N PRO A 367 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.30e-02 5.92e+03 3.48e+00 bond pdb=" C1 GYP A 701 " pdb=" O5 GYP A 701 " ideal model delta sigma weight residual 1.400 1.431 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C2 GYP A 701 " pdb=" O2 GYP A 701 " ideal model delta sigma weight residual 1.402 1.430 -0.028 2.00e-02 2.50e+03 1.92e+00 bond pdb=" C6 GYP A 701 " pdb=" O6 GYP A 701 " ideal model delta sigma weight residual 1.407 1.432 -0.025 2.00e-02 2.50e+03 1.56e+00 ... (remaining 4486 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 6017 2.18 - 4.36: 115 4.36 - 6.55: 11 6.55 - 8.73: 3 8.73 - 10.91: 1 Bond angle restraints: 6147 Sorted by residual: angle pdb=" C LEU A 322 " pdb=" N THR A 323 " pdb=" CA THR A 323 " ideal model delta sigma weight residual 120.09 131.00 -10.91 1.25e+00 6.40e-01 7.62e+01 angle pdb=" N VAL A 346 " pdb=" CA VAL A 346 " pdb=" C VAL A 346 " ideal model delta sigma weight residual 113.71 109.69 4.02 9.50e-01 1.11e+00 1.79e+01 angle pdb=" N VAL A 248 " pdb=" CA VAL A 248 " pdb=" C VAL A 248 " ideal model delta sigma weight residual 113.53 109.83 3.70 9.80e-01 1.04e+00 1.43e+01 angle pdb=" N THR A 323 " pdb=" CA THR A 323 " pdb=" C THR A 323 " ideal model delta sigma weight residual 113.16 116.81 -3.65 1.42e+00 4.96e-01 6.62e+00 angle pdb=" C THR A 548 " pdb=" N ALA A 549 " pdb=" CA ALA A 549 " ideal model delta sigma weight residual 120.65 123.82 -3.17 1.36e+00 5.41e-01 5.44e+00 ... (remaining 6142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 2361 17.54 - 35.08: 163 35.08 - 52.62: 42 52.62 - 70.16: 3 70.16 - 87.70: 3 Dihedral angle restraints: 2572 sinusoidal: 884 harmonic: 1688 Sorted by residual: dihedral pdb=" CB CYS A 517 " pdb=" SG CYS A 517 " pdb=" SG CYS A 522 " pdb=" CB CYS A 522 " ideal model delta sinusoidal sigma weight residual -86.00 -154.35 68.35 1 1.00e+01 1.00e-02 6.06e+01 dihedral pdb=" CB CYS A 255 " pdb=" SG CYS A 255 " pdb=" SG CYS A 511 " pdb=" CB CYS A 511 " ideal model delta sinusoidal sigma weight residual 93.00 156.87 -63.87 1 1.00e+01 1.00e-02 5.37e+01 dihedral pdb=" CB CYS A 355 " pdb=" SG CYS A 355 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 145.25 -52.25 1 1.00e+01 1.00e-02 3.72e+01 ... (remaining 2569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 518 0.045 - 0.089: 183 0.089 - 0.134: 28 0.134 - 0.178: 3 0.178 - 0.223: 1 Chirality restraints: 733 Sorted by residual: chirality pdb=" CG LEU A 322 " pdb=" CB LEU A 322 " pdb=" CD1 LEU A 322 " pdb=" CD2 LEU A 322 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA PHE A 152 " pdb=" N PHE A 152 " pdb=" C PHE A 152 " pdb=" CB PHE A 152 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA TRP A 65 " pdb=" N TRP A 65 " pdb=" C TRP A 65 " pdb=" CB TRP A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 730 not shown) Planarity restraints: 748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 465 " -0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO A 466 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 466 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 466 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 279 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C LEU A 279 " 0.036 2.00e-02 2.50e+03 pdb=" O LEU A 279 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 280 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 501 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO A 502 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 502 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 502 " -0.028 5.00e-02 4.00e+02 ... (remaining 745 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 975 2.78 - 3.31: 4495 3.31 - 3.84: 7593 3.84 - 4.37: 8107 4.37 - 4.90: 14496 Nonbonded interactions: 35666 Sorted by model distance: nonbonded pdb=" O ILE A 501 " pdb=" OG SER A 505 " model vdw 2.249 3.040 nonbonded pdb=" O PHE A 561 " pdb=" NH1 ARG A 564 " model vdw 2.267 3.120 nonbonded pdb=" OH TYR A 128 " pdb=" O LEU A 559 " model vdw 2.286 3.040 nonbonded pdb=" O PHE A 220 " pdb=" N GLY A 225 " model vdw 2.303 3.120 nonbonded pdb=" O GLY A 86 " pdb=" OG SER A 362 " model vdw 2.351 3.040 ... (remaining 35661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.330 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.110 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 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 : 0.004 0.046 4495 Z= 0.160 Angle : 0.680 10.909 6155 Z= 0.366 Chirality : 0.043 0.223 733 Planarity : 0.005 0.054 748 Dihedral : 12.776 87.697 1482 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.41 (0.35), residues: 582 helix: 1.67 (0.26), residues: 417 sheet: None (None), residues: 0 loop : -0.94 (0.48), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 257 TYR 0.011 0.001 TYR A 128 PHE 0.012 0.001 PHE A 113 TRP 0.011 0.001 TRP A 65 HIS 0.002 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4491) covalent geometry : angle 0.67896 ( 6147) SS BOND : bond 0.00044 ( 4) SS BOND : angle 1.18563 ( 8) hydrogen bonds : bond 0.13517 ( 320) hydrogen bonds : angle 6.39249 ( 948) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.162 Fit side-chains REVERT: A 325 MET cc_start: 0.6917 (tmm) cc_final: 0.5623 (tmm) REVERT: A 535 PHE cc_start: 0.6590 (m-80) cc_final: 0.6311 (m-10) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0384 time to fit residues: 4.6121 Evaluate side-chains 72 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.0370 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 7.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.179847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.158114 restraints weight = 5349.013| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.31 r_work: 0.3814 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4495 Z= 0.150 Angle : 0.611 6.395 6155 Z= 0.312 Chirality : 0.044 0.162 733 Planarity : 0.005 0.048 748 Dihedral : 4.017 16.593 655 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.83 % Allowed : 8.96 % Favored : 88.21 % 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: 1.49 (0.36), residues: 582 helix: 1.56 (0.25), residues: 426 sheet: None (None), residues: 0 loop : -0.53 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 352 TYR 0.017 0.002 TYR A 339 PHE 0.027 0.002 PHE A 504 TRP 0.010 0.001 TRP A 65 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 4491) covalent geometry : angle 0.60999 ( 6147) SS BOND : bond 0.00256 ( 4) SS BOND : angle 0.98196 ( 8) hydrogen bonds : bond 0.03742 ( 320) hydrogen bonds : angle 4.92778 ( 948) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.104 Fit side-chains REVERT: A 151 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7703 (mp) REVERT: A 325 MET cc_start: 0.7253 (tmm) cc_final: 0.5861 (tmm) REVERT: A 535 PHE cc_start: 0.6690 (m-80) cc_final: 0.6460 (m-10) outliers start: 12 outliers final: 11 residues processed: 76 average time/residue: 0.0420 time to fit residues: 4.3519 Evaluate side-chains 83 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 655 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 42 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 0.0050 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 0.3980 chunk 23 optimal weight: 0.0030 chunk 7 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.2404 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.182662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.161049 restraints weight = 5299.680| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.26 r_work: 0.3787 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4495 Z= 0.119 Angle : 0.549 6.282 6155 Z= 0.282 Chirality : 0.041 0.136 733 Planarity : 0.005 0.048 748 Dihedral : 3.811 20.116 655 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.36 % Allowed : 13.44 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.69 (0.36), residues: 582 helix: 1.69 (0.25), residues: 427 sheet: None (None), residues: 0 loop : -0.39 (0.54), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 564 TYR 0.010 0.001 TYR A 339 PHE 0.019 0.001 PHE A 504 TRP 0.011 0.001 TRP A 289 HIS 0.002 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4491) covalent geometry : angle 0.54887 ( 6147) SS BOND : bond 0.00185 ( 4) SS BOND : angle 0.69771 ( 8) hydrogen bonds : bond 0.03334 ( 320) hydrogen bonds : angle 4.70896 ( 948) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.096 Fit side-chains REVERT: A 151 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7873 (mp) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.0397 time to fit residues: 4.1771 Evaluate side-chains 77 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 655 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 chunk 55 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.177092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.155379 restraints weight = 5222.092| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.25 r_work: 0.3777 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4495 Z= 0.147 Angle : 0.587 6.359 6155 Z= 0.301 Chirality : 0.042 0.149 733 Planarity : 0.005 0.051 748 Dihedral : 3.916 15.792 655 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.07 % Allowed : 16.98 % Favored : 79.95 % 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: 1.55 (0.36), residues: 582 helix: 1.58 (0.25), residues: 425 sheet: None (None), residues: 0 loop : -0.39 (0.55), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 352 TYR 0.015 0.002 TYR A 671 PHE 0.019 0.002 PHE A 504 TRP 0.011 0.001 TRP A 289 HIS 0.001 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 4491) covalent geometry : angle 0.58670 ( 6147) SS BOND : bond 0.00241 ( 4) SS BOND : angle 0.86752 ( 8) hydrogen bonds : bond 0.03585 ( 320) hydrogen bonds : angle 4.63763 ( 948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 394 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6979 (mp) REVERT: A 448 GLN cc_start: 0.7521 (mm110) cc_final: 0.7269 (mm110) outliers start: 13 outliers final: 9 residues processed: 83 average time/residue: 0.0513 time to fit residues: 5.6380 Evaluate side-chains 83 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 9 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 0.2980 chunk 39 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.177076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.155091 restraints weight = 5298.074| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.26 r_work: 0.3778 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4495 Z= 0.143 Angle : 0.596 6.754 6155 Z= 0.303 Chirality : 0.043 0.241 733 Planarity : 0.005 0.052 748 Dihedral : 3.885 16.582 655 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.77 % Allowed : 17.92 % Favored : 78.30 % 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: 1.55 (0.36), residues: 582 helix: 1.58 (0.25), residues: 424 sheet: None (None), residues: 0 loop : -0.40 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 352 TYR 0.012 0.001 TYR A 141 PHE 0.017 0.001 PHE A 504 TRP 0.013 0.001 TRP A 289 HIS 0.002 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 4491) covalent geometry : angle 0.59512 ( 6147) SS BOND : bond 0.00231 ( 4) SS BOND : angle 0.90618 ( 8) hydrogen bonds : bond 0.03461 ( 320) hydrogen bonds : angle 4.60921 ( 948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.150 Fit side-chains REVERT: A 394 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.7014 (mp) REVERT: A 448 GLN cc_start: 0.7543 (mm110) cc_final: 0.7300 (mm110) outliers start: 16 outliers final: 13 residues processed: 84 average time/residue: 0.0484 time to fit residues: 5.5624 Evaluate side-chains 89 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.174762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.152933 restraints weight = 5401.153| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.28 r_work: 0.3751 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4495 Z= 0.153 Angle : 0.597 6.325 6155 Z= 0.305 Chirality : 0.043 0.228 733 Planarity : 0.005 0.052 748 Dihedral : 3.913 16.869 655 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.95 % Allowed : 18.16 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.41 (0.36), residues: 582 helix: 1.50 (0.25), residues: 423 sheet: None (None), residues: 0 loop : -0.49 (0.55), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 564 TYR 0.012 0.001 TYR A 141 PHE 0.027 0.002 PHE A 504 TRP 0.012 0.001 TRP A 289 HIS 0.002 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 4491) covalent geometry : angle 0.59609 ( 6147) SS BOND : bond 0.00238 ( 4) SS BOND : angle 0.96710 ( 8) hydrogen bonds : bond 0.03584 ( 320) hydrogen bonds : angle 4.62297 ( 948) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.141 Fit side-chains REVERT: A 64 TRP cc_start: 0.8354 (p-90) cc_final: 0.8028 (p-90) REVERT: A 328 MET cc_start: 0.6707 (OUTLIER) cc_final: 0.6211 (mpp) REVERT: A 394 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7020 (mp) REVERT: A 448 GLN cc_start: 0.7572 (mm110) cc_final: 0.7328 (mm110) outliers start: 21 outliers final: 16 residues processed: 87 average time/residue: 0.0509 time to fit residues: 5.9218 Evaluate side-chains 92 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 47 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.175636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.153680 restraints weight = 5380.494| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.29 r_work: 0.3767 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4495 Z= 0.134 Angle : 0.578 6.222 6155 Z= 0.294 Chirality : 0.042 0.214 733 Planarity : 0.005 0.052 748 Dihedral : 3.852 16.239 655 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.01 % Allowed : 20.28 % Favored : 75.71 % 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: 1.52 (0.36), residues: 582 helix: 1.58 (0.25), residues: 424 sheet: None (None), residues: 0 loop : -0.47 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 564 TYR 0.015 0.001 TYR A 175 PHE 0.024 0.001 PHE A 504 TRP 0.013 0.001 TRP A 289 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4491) covalent geometry : angle 0.57731 ( 6147) SS BOND : bond 0.00220 ( 4) SS BOND : angle 0.86611 ( 8) hydrogen bonds : bond 0.03394 ( 320) hydrogen bonds : angle 4.56818 ( 948) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.207 Fit side-chains REVERT: A 64 TRP cc_start: 0.8296 (p-90) cc_final: 0.7998 (p-90) REVERT: A 328 MET cc_start: 0.6658 (mpp) cc_final: 0.6168 (mtt) REVERT: A 394 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6978 (mp) REVERT: A 448 GLN cc_start: 0.7561 (mm110) cc_final: 0.7308 (mm110) outliers start: 17 outliers final: 14 residues processed: 83 average time/residue: 0.0482 time to fit residues: 5.4228 Evaluate side-chains 88 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 0.0040 chunk 8 optimal weight: 0.0370 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.4670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.175715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.154016 restraints weight = 5400.245| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.27 r_work: 0.3780 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 4495 Z= 0.131 Angle : 0.583 6.172 6155 Z= 0.300 Chirality : 0.042 0.208 733 Planarity : 0.005 0.052 748 Dihedral : 3.850 17.961 655 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.48 % Allowed : 21.23 % Favored : 74.29 % 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: 1.54 (0.36), residues: 582 helix: 1.60 (0.25), residues: 424 sheet: None (None), residues: 0 loop : -0.50 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 564 TYR 0.014 0.001 TYR A 175 PHE 0.023 0.001 PHE A 504 TRP 0.013 0.001 TRP A 289 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 4491) covalent geometry : angle 0.58250 ( 6147) SS BOND : bond 0.00204 ( 4) SS BOND : angle 0.78388 ( 8) hydrogen bonds : bond 0.03349 ( 320) hydrogen bonds : angle 4.57081 ( 948) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.170 Fit side-chains REVERT: A 64 TRP cc_start: 0.8241 (p-90) cc_final: 0.7933 (p-90) REVERT: A 328 MET cc_start: 0.6677 (OUTLIER) cc_final: 0.6211 (mtt) REVERT: A 394 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7068 (mp) REVERT: A 448 GLN cc_start: 0.7546 (mm110) cc_final: 0.7301 (mm110) outliers start: 19 outliers final: 16 residues processed: 82 average time/residue: 0.0504 time to fit residues: 5.5477 Evaluate side-chains 91 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 34 optimal weight: 0.0370 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 50 optimal weight: 0.0970 chunk 52 optimal weight: 0.5980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.178880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.156815 restraints weight = 5338.291| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.33 r_work: 0.3798 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4495 Z= 0.122 Angle : 0.575 6.562 6155 Z= 0.293 Chirality : 0.041 0.201 733 Planarity : 0.005 0.053 748 Dihedral : 3.798 19.667 655 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.01 % Allowed : 21.23 % Favored : 74.76 % 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: 1.72 (0.36), residues: 582 helix: 1.75 (0.25), residues: 424 sheet: None (None), residues: 0 loop : -0.47 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 564 TYR 0.013 0.001 TYR A 175 PHE 0.022 0.001 PHE A 504 TRP 0.013 0.001 TRP A 289 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4491) covalent geometry : angle 0.57458 ( 6147) SS BOND : bond 0.00193 ( 4) SS BOND : angle 0.72074 ( 8) hydrogen bonds : bond 0.03174 ( 320) hydrogen bonds : angle 4.50247 ( 948) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.147 Fit side-chains REVERT: A 64 TRP cc_start: 0.8229 (p-90) cc_final: 0.7908 (p-90) REVERT: A 328 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.6061 (mtt) REVERT: A 448 GLN cc_start: 0.7557 (mm110) cc_final: 0.7300 (mm110) outliers start: 17 outliers final: 14 residues processed: 81 average time/residue: 0.0402 time to fit residues: 4.4056 Evaluate side-chains 86 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 0.0040 chunk 56 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.175939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.154247 restraints weight = 5379.152| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.26 r_work: 0.3771 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 4495 Z= 0.135 Angle : 0.593 6.962 6155 Z= 0.301 Chirality : 0.042 0.202 733 Planarity : 0.005 0.053 748 Dihedral : 3.859 19.021 655 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.07 % Allowed : 22.17 % Favored : 74.76 % 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: 1.67 (0.36), residues: 582 helix: 1.71 (0.25), residues: 424 sheet: None (None), residues: 0 loop : -0.48 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 564 TYR 0.013 0.001 TYR A 175 PHE 0.023 0.001 PHE A 504 TRP 0.012 0.001 TRP A 289 HIS 0.002 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4491) covalent geometry : angle 0.59312 ( 6147) SS BOND : bond 0.00187 ( 4) SS BOND : angle 0.71180 ( 8) hydrogen bonds : bond 0.03331 ( 320) hydrogen bonds : angle 4.53553 ( 948) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.166 Fit side-chains REVERT: A 64 TRP cc_start: 0.8241 (p-90) cc_final: 0.7938 (p-90) REVERT: A 328 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.6122 (mtt) REVERT: A 394 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6982 (mp) REVERT: A 448 GLN cc_start: 0.7433 (mm110) cc_final: 0.7174 (mm110) outliers start: 13 outliers final: 10 residues processed: 79 average time/residue: 0.0441 time to fit residues: 4.7939 Evaluate side-chains 85 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.174768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.153244 restraints weight = 5311.006| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.26 r_work: 0.3747 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4495 Z= 0.148 Angle : 0.611 6.888 6155 Z= 0.311 Chirality : 0.043 0.206 733 Planarity : 0.005 0.052 748 Dihedral : 3.926 17.576 655 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.07 % Allowed : 22.17 % Favored : 74.76 % 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: 1.58 (0.36), residues: 582 helix: 1.66 (0.25), residues: 423 sheet: None (None), residues: 0 loop : -0.53 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 564 TYR 0.013 0.001 TYR A 175 PHE 0.023 0.002 PHE A 504 TRP 0.011 0.001 TRP A 289 HIS 0.002 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 4491) covalent geometry : angle 0.61089 ( 6147) SS BOND : bond 0.00202 ( 4) SS BOND : angle 0.76704 ( 8) hydrogen bonds : bond 0.03464 ( 320) hydrogen bonds : angle 4.57950 ( 948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 912.04 seconds wall clock time: 16 minutes 19.30 seconds (979.30 seconds total)