Starting phenix.real_space_refine on Fri Aug 22 13:42:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kb4_37069/08_2025/8kb4_37069_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kb4_37069/08_2025/8kb4_37069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kb4_37069/08_2025/8kb4_37069_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kb4_37069/08_2025/8kb4_37069_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kb4_37069/08_2025/8kb4_37069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kb4_37069/08_2025/8kb4_37069.map" } resolution = 3.1 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= -0.000 sd= 0.013 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 20 5.16 5 C 2234 2.51 5 N 535 2.21 5 O 577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 3367 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3293 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 11, 'TRANS': 390} Chain breaks: 2 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 74 Unusual residues: {'65I': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.22, per 1000 atoms: 0.36 Number of scatterers: 3367 At special positions: 0 Unit cell: (57.664, 66.992, 112.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 1 15.00 O 577 8.00 N 535 7.00 C 2234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 431 " distance=2.04 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 Links applied NAG-ASN " NAG A 901 " - " ASN A 79 " " NAG A 902 " - " ASN A 127 " Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 161.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 2 sheets defined 54.7% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 90 through 95 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 100 through 110 removed outlier: 4.080A pdb=" N GLU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 251 Processing helix chain 'A' and resid 256 through 287 removed outlier: 3.501A pdb=" N PHE A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 318 Processing helix chain 'A' and resid 326 through 331 removed outlier: 4.259A pdb=" N LEU A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 337 Processing helix chain 'A' and resid 338 through 354 removed outlier: 4.198A pdb=" N LEU A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 350 " --> pdb=" O MET A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 393 removed outlier: 4.277A pdb=" N LEU A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 427 removed outlier: 3.643A pdb=" N SER A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 442 Processing helix chain 'A' and resid 443 through 460 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 44 removed outlier: 3.713A pdb=" N ASP A 70 " --> pdb=" O THR A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 59 removed outlier: 3.974A pdb=" N SER A 77 " --> pdb=" O SER A 191 " (cutoff:3.500A) 197 hydrogen bonds defined for protein. 576 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: 0.35 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 493 1.31 - 1.43: 1013 1.43 - 1.56: 1913 1.56 - 1.69: 2 1.69 - 1.81: 33 Bond restraints: 3454 Sorted by residual: bond pdb=" C11 65I A 903 " pdb=" O6 65I A 903 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C5 65I A 903 " pdb=" O1 65I A 903 " ideal model delta sigma weight residual 1.335 1.400 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 NAG A 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.81e+00 bond pdb=" C7 65I A 903 " pdb=" O6 65I A 903 " ideal model delta sigma weight residual 1.429 1.399 0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C6 65I A 903 " pdb=" O1 65I A 903 " ideal model delta sigma weight residual 1.427 1.399 0.028 2.00e-02 2.50e+03 1.95e+00 ... (remaining 3449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.33: 4666 4.33 - 8.67: 7 8.67 - 13.00: 3 13.00 - 17.34: 0 17.34 - 21.67: 1 Bond angle restraints: 4677 Sorted by residual: angle pdb=" C17 65I A 903 " pdb=" C18 65I A 903 " pdb=" C19 65I A 903 " ideal model delta sigma weight residual 114.14 135.81 -21.67 3.00e+00 1.11e-01 5.22e+01 angle pdb=" C THR A 357 " pdb=" N ASP A 358 " pdb=" CA ASP A 358 " ideal model delta sigma weight residual 122.61 130.38 -7.77 1.56e+00 4.11e-01 2.48e+01 angle pdb=" O3 65I A 903 " pdb=" P 65I A 903 " pdb=" O4 65I A 903 " ideal model delta sigma weight residual 122.02 109.40 12.62 3.00e+00 1.11e-01 1.77e+01 angle pdb=" O2 65I A 903 " pdb=" P 65I A 903 " pdb=" O5 65I A 903 " ideal model delta sigma weight residual 98.05 109.63 -11.58 3.00e+00 1.11e-01 1.49e+01 angle pdb=" N ASP A 75 " pdb=" CA ASP A 75 " pdb=" C ASP A 75 " ideal model delta sigma weight residual 113.18 108.39 4.79 1.33e+00 5.65e-01 1.30e+01 ... (remaining 4672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.61: 1924 25.61 - 51.22: 112 51.22 - 76.82: 18 76.82 - 102.43: 9 102.43 - 128.04: 6 Dihedral angle restraints: 2069 sinusoidal: 889 harmonic: 1180 Sorted by residual: dihedral pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " pdb=" SG CYS A 128 " pdb=" CB CYS A 128 " ideal model delta sinusoidal sigma weight residual -86.00 -37.98 -48.02 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" C2 65I A 903 " pdb=" C3 65I A 903 " pdb=" C4 65I A 903 " pdb=" C5 65I A 903 " ideal model delta sinusoidal sigma weight residual -173.23 -45.19 -128.04 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" C2 NAG A 902 " pdb=" C1 NAG A 902 " pdb=" O5 NAG A 902 " pdb=" C5 NAG A 902 " ideal model delta sinusoidal sigma weight residual -62.96 60.58 -123.54 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 2066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 361 0.031 - 0.062: 127 0.062 - 0.092: 32 0.092 - 0.123: 10 0.123 - 0.154: 5 Chirality restraints: 535 Sorted by residual: chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 127 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA ILE A 183 " pdb=" N ILE A 183 " pdb=" C ILE A 183 " pdb=" CB ILE A 183 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ASP A 358 " pdb=" N ASP A 358 " pdb=" C ASP A 358 " pdb=" CB ASP A 358 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 532 not shown) Planarity restraints: 557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 72 " -0.031 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO A 73 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 357 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C THR A 357 " 0.029 2.00e-02 2.50e+03 pdb=" O THR A 357 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP A 358 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 221 " -0.005 2.00e-02 2.50e+03 9.91e-03 9.81e-01 pdb=" C LEU A 221 " 0.017 2.00e-02 2.50e+03 pdb=" O LEU A 221 " -0.006 2.00e-02 2.50e+03 pdb=" N GLU A 222 " -0.006 2.00e-02 2.50e+03 ... (remaining 554 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 77 2.70 - 3.25: 3391 3.25 - 3.80: 5040 3.80 - 4.35: 5860 4.35 - 4.90: 10338 Nonbonded interactions: 24706 Sorted by model distance: nonbonded pdb=" N GLU A 217 " pdb=" OE1 GLU A 217 " model vdw 2.151 3.120 nonbonded pdb=" O THR A 357 " pdb=" OD1 ASP A 358 " model vdw 2.207 3.040 nonbonded pdb=" N GLY A 71 " pdb=" OE2 GLU A 130 " model vdw 2.231 3.120 nonbonded pdb=" O GLN A 178 " pdb=" OH TYR A 182 " model vdw 2.256 3.040 nonbonded pdb=" OD1 ASN A 91 " pdb=" N GLU A 92 " model vdw 2.266 3.120 ... (remaining 24701 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: 1.290 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.080 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 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 0.069 3458 Z= 0.201 Angle : 0.705 21.673 4687 Z= 0.323 Chirality : 0.037 0.154 535 Planarity : 0.003 0.048 555 Dihedral : 19.096 128.040 1299 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 1.68 (0.47), residues: 396 helix: 3.28 (0.38), residues: 204 sheet: 0.04 (0.68), residues: 67 loop : -2.19 (0.54), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 39 TYR 0.009 0.001 TYR A 104 PHE 0.010 0.001 PHE A 379 TRP 0.008 0.001 TRP A 247 HIS 0.002 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 3454) covalent geometry : angle 0.70339 ( 4677) SS BOND : bond 0.00600 ( 2) SS BOND : angle 0.93104 ( 4) hydrogen bonds : bond 0.12354 ( 197) hydrogen bonds : angle 5.00491 ( 576) link_NAG-ASN : bond 0.00262 ( 2) link_NAG-ASN : angle 1.36210 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: A 434 ASP cc_start: 0.8624 (p0) cc_final: 0.8414 (p0) REVERT: A 465 ASN cc_start: 0.9337 (t0) cc_final: 0.9035 (t0) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0453 time to fit residues: 2.8468 Evaluate side-chains 39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.114708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.086929 restraints weight = 5554.301| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.22 r_work: 0.3024 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3458 Z= 0.129 Angle : 0.604 7.168 4687 Z= 0.300 Chirality : 0.040 0.170 535 Planarity : 0.004 0.065 555 Dihedral : 16.545 106.116 533 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.28 % Allowed : 6.16 % Favored : 93.56 % 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: 2.25 (0.47), residues: 396 helix: 3.80 (0.37), residues: 204 sheet: 0.60 (0.68), residues: 63 loop : -2.15 (0.54), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 351 TYR 0.017 0.002 TYR A 340 PHE 0.011 0.001 PHE A 55 TRP 0.007 0.001 TRP A 252 HIS 0.003 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 3454) covalent geometry : angle 0.59310 ( 4677) SS BOND : bond 0.00544 ( 2) SS BOND : angle 0.97939 ( 4) hydrogen bonds : bond 0.04565 ( 197) hydrogen bonds : angle 3.27658 ( 576) link_NAG-ASN : bond 0.00541 ( 2) link_NAG-ASN : angle 3.14228 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: A 141 PHE cc_start: 0.7593 (m-10) cc_final: 0.7320 (m-80) REVERT: A 465 ASN cc_start: 0.9437 (t0) cc_final: 0.9074 (t0) outliers start: 1 outliers final: 1 residues processed: 42 average time/residue: 0.0577 time to fit residues: 3.1644 Evaluate side-chains 37 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.113246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.085697 restraints weight = 5625.995| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.27 r_work: 0.3008 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3458 Z= 0.122 Angle : 0.587 9.497 4687 Z= 0.281 Chirality : 0.039 0.165 535 Planarity : 0.004 0.065 555 Dihedral : 14.528 102.824 533 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.84 % Allowed : 9.80 % Favored : 89.36 % 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: 2.22 (0.46), residues: 396 helix: 3.75 (0.37), residues: 206 sheet: 0.70 (0.67), residues: 63 loop : -2.29 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 402 TYR 0.011 0.001 TYR A 340 PHE 0.011 0.001 PHE A 55 TRP 0.005 0.001 TRP A 82 HIS 0.002 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 3454) covalent geometry : angle 0.57706 ( 4677) SS BOND : bond 0.00709 ( 2) SS BOND : angle 1.06406 ( 4) hydrogen bonds : bond 0.04494 ( 197) hydrogen bonds : angle 3.15028 ( 576) link_NAG-ASN : bond 0.00377 ( 2) link_NAG-ASN : angle 3.03005 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.161 Fit side-chains REVERT: A 141 PHE cc_start: 0.7618 (m-10) cc_final: 0.7222 (m-80) REVERT: A 442 ASP cc_start: 0.8746 (m-30) cc_final: 0.8453 (m-30) REVERT: A 465 ASN cc_start: 0.9476 (t0) cc_final: 0.9097 (t0) outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 0.0506 time to fit residues: 2.3778 Evaluate side-chains 36 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.111198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.083551 restraints weight = 5559.971| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.28 r_work: 0.2978 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3458 Z= 0.151 Angle : 0.583 7.364 4687 Z= 0.281 Chirality : 0.040 0.203 535 Planarity : 0.004 0.063 555 Dihedral : 13.436 96.260 533 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.40 % Allowed : 10.08 % Favored : 88.52 % 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: 2.12 (0.46), residues: 396 helix: 3.66 (0.36), residues: 206 sheet: 0.76 (0.67), residues: 63 loop : -2.38 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 436 TYR 0.012 0.001 TYR A 340 PHE 0.014 0.001 PHE A 55 TRP 0.006 0.001 TRP A 82 HIS 0.002 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 3454) covalent geometry : angle 0.57119 ( 4677) SS BOND : bond 0.00607 ( 2) SS BOND : angle 1.35620 ( 4) hydrogen bonds : bond 0.05178 ( 197) hydrogen bonds : angle 3.22279 ( 576) link_NAG-ASN : bond 0.00272 ( 2) link_NAG-ASN : angle 3.20701 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.109 Fit side-chains REVERT: A 141 PHE cc_start: 0.7800 (m-10) cc_final: 0.7498 (m-80) REVERT: A 442 ASP cc_start: 0.8751 (m-30) cc_final: 0.8449 (m-30) REVERT: A 465 ASN cc_start: 0.9473 (t0) cc_final: 0.9084 (t0) outliers start: 5 outliers final: 2 residues processed: 37 average time/residue: 0.0596 time to fit residues: 2.7833 Evaluate side-chains 35 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.0050 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.113532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.086011 restraints weight = 5523.672| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.26 r_work: 0.3018 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3458 Z= 0.110 Angle : 0.552 7.606 4687 Z= 0.265 Chirality : 0.038 0.166 535 Planarity : 0.004 0.063 555 Dihedral : 12.473 89.928 533 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.84 % Allowed : 12.04 % Favored : 87.11 % 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: 2.23 (0.46), residues: 396 helix: 3.77 (0.37), residues: 206 sheet: 0.80 (0.66), residues: 63 loop : -2.37 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 402 TYR 0.011 0.001 TYR A 340 PHE 0.010 0.001 PHE A 55 TRP 0.006 0.001 TRP A 82 HIS 0.002 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 3454) covalent geometry : angle 0.53628 ( 4677) SS BOND : bond 0.00701 ( 2) SS BOND : angle 1.27681 ( 4) hydrogen bonds : bond 0.04273 ( 197) hydrogen bonds : angle 3.07288 ( 576) link_NAG-ASN : bond 0.00295 ( 2) link_NAG-ASN : angle 3.62235 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.090 Fit side-chains REVERT: A 141 PHE cc_start: 0.7869 (m-10) cc_final: 0.7463 (m-80) REVERT: A 442 ASP cc_start: 0.8769 (m-30) cc_final: 0.8485 (m-30) REVERT: A 465 ASN cc_start: 0.9476 (t0) cc_final: 0.9085 (t0) outliers start: 3 outliers final: 3 residues processed: 38 average time/residue: 0.0495 time to fit residues: 2.4991 Evaluate side-chains 39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.0370 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.112436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.084744 restraints weight = 5603.259| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.28 r_work: 0.2992 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3458 Z= 0.126 Angle : 0.550 7.540 4687 Z= 0.267 Chirality : 0.038 0.177 535 Planarity : 0.004 0.062 555 Dihedral : 11.970 88.410 533 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.96 % Allowed : 12.32 % Favored : 85.71 % 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: 2.20 (0.46), residues: 396 helix: 3.75 (0.36), residues: 206 sheet: 0.82 (0.66), residues: 63 loop : -2.42 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 144 TYR 0.010 0.001 TYR A 340 PHE 0.012 0.001 PHE A 55 TRP 0.006 0.001 TRP A 82 HIS 0.002 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 3454) covalent geometry : angle 0.53580 ( 4677) SS BOND : bond 0.00635 ( 2) SS BOND : angle 0.99228 ( 4) hydrogen bonds : bond 0.04637 ( 197) hydrogen bonds : angle 3.11873 ( 576) link_NAG-ASN : bond 0.00187 ( 2) link_NAG-ASN : angle 3.49885 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.134 Fit side-chains REVERT: A 141 PHE cc_start: 0.7954 (m-10) cc_final: 0.7695 (m-80) REVERT: A 437 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8472 (pm20) REVERT: A 442 ASP cc_start: 0.8769 (m-30) cc_final: 0.8493 (m-30) REVERT: A 465 ASN cc_start: 0.9484 (t0) cc_final: 0.9086 (t0) outliers start: 7 outliers final: 4 residues processed: 43 average time/residue: 0.0446 time to fit residues: 2.6045 Evaluate side-chains 38 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.112851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.084994 restraints weight = 5602.947| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.31 r_work: 0.3013 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3458 Z= 0.122 Angle : 0.542 7.555 4687 Z= 0.263 Chirality : 0.038 0.175 535 Planarity : 0.004 0.061 555 Dihedral : 11.645 86.420 533 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.68 % Allowed : 12.32 % Favored : 85.99 % 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: 2.11 (0.46), residues: 396 helix: 3.67 (0.37), residues: 206 sheet: 0.80 (0.67), residues: 63 loop : -2.44 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.010 0.001 TYR A 340 PHE 0.011 0.001 PHE A 55 TRP 0.006 0.001 TRP A 82 HIS 0.002 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3454) covalent geometry : angle 0.52632 ( 4677) SS BOND : bond 0.00602 ( 2) SS BOND : angle 0.99099 ( 4) hydrogen bonds : bond 0.04532 ( 197) hydrogen bonds : angle 3.13920 ( 576) link_NAG-ASN : bond 0.00190 ( 2) link_NAG-ASN : angle 3.55070 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.122 Fit side-chains REVERT: A 141 PHE cc_start: 0.7971 (m-10) cc_final: 0.7569 (m-80) REVERT: A 442 ASP cc_start: 0.8768 (m-30) cc_final: 0.8504 (m-30) REVERT: A 465 ASN cc_start: 0.9474 (t0) cc_final: 0.9082 (t0) outliers start: 6 outliers final: 3 residues processed: 40 average time/residue: 0.0553 time to fit residues: 2.9234 Evaluate side-chains 39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 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 = 0.3605 r_free = 0.3605 target = 0.112226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.084677 restraints weight = 5651.587| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.29 r_work: 0.2997 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3458 Z= 0.126 Angle : 0.562 9.870 4687 Z= 0.270 Chirality : 0.040 0.265 535 Planarity : 0.004 0.062 555 Dihedral : 11.343 86.168 533 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.40 % Allowed : 13.73 % Favored : 84.87 % 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: 2.08 (0.46), residues: 396 helix: 3.66 (0.37), residues: 206 sheet: 0.78 (0.66), residues: 63 loop : -2.49 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.012 0.001 TYR A 83 PHE 0.012 0.001 PHE A 55 TRP 0.007 0.001 TRP A 82 HIS 0.002 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 3454) covalent geometry : angle 0.52559 ( 4677) SS BOND : bond 0.00511 ( 2) SS BOND : angle 1.19372 ( 4) hydrogen bonds : bond 0.04587 ( 197) hydrogen bonds : angle 3.14383 ( 576) link_NAG-ASN : bond 0.00538 ( 2) link_NAG-ASN : angle 5.50043 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: A 141 PHE cc_start: 0.7999 (m-10) cc_final: 0.7760 (m-80) REVERT: A 465 ASN cc_start: 0.9477 (t0) cc_final: 0.9113 (t0) outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 0.0418 time to fit residues: 2.1726 Evaluate side-chains 40 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.111810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.084244 restraints weight = 5608.858| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.28 r_work: 0.2986 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3458 Z= 0.139 Angle : 0.570 8.882 4687 Z= 0.278 Chirality : 0.040 0.233 535 Planarity : 0.004 0.061 555 Dihedral : 11.160 91.084 533 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.12 % Allowed : 15.13 % Favored : 83.75 % 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: 2.05 (0.46), residues: 396 helix: 3.64 (0.37), residues: 206 sheet: 0.76 (0.66), residues: 63 loop : -2.52 (0.49), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.014 0.001 TYR A 83 PHE 0.012 0.001 PHE A 55 TRP 0.006 0.001 TRP A 82 HIS 0.002 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 3454) covalent geometry : angle 0.54172 ( 4677) SS BOND : bond 0.00540 ( 2) SS BOND : angle 1.21104 ( 4) hydrogen bonds : bond 0.04860 ( 197) hydrogen bonds : angle 3.17976 ( 576) link_NAG-ASN : bond 0.00595 ( 2) link_NAG-ASN : angle 4.92175 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.163 Fit side-chains REVERT: A 141 PHE cc_start: 0.8002 (m-10) cc_final: 0.7590 (m-80) REVERT: A 441 ASP cc_start: 0.8650 (p0) cc_final: 0.8330 (p0) REVERT: A 442 ASP cc_start: 0.8783 (m-30) cc_final: 0.8490 (m-30) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.0574 time to fit residues: 2.9511 Evaluate side-chains 37 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.111006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.083416 restraints weight = 5680.233| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.30 r_work: 0.2970 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3458 Z= 0.155 Angle : 0.574 7.643 4687 Z= 0.283 Chirality : 0.040 0.218 535 Planarity : 0.004 0.061 555 Dihedral : 11.137 94.086 533 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.12 % Allowed : 15.13 % Favored : 83.75 % 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: 1.99 (0.46), residues: 396 helix: 3.58 (0.36), residues: 206 sheet: 0.77 (0.66), residues: 63 loop : -2.54 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.012 0.001 TYR A 83 PHE 0.013 0.001 PHE A 55 TRP 0.007 0.001 TRP A 82 HIS 0.002 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 3454) covalent geometry : angle 0.55123 ( 4677) SS BOND : bond 0.00551 ( 2) SS BOND : angle 1.30016 ( 4) hydrogen bonds : bond 0.05212 ( 197) hydrogen bonds : angle 3.24498 ( 576) link_NAG-ASN : bond 0.00490 ( 2) link_NAG-ASN : angle 4.35569 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.109 Fit side-chains REVERT: A 141 PHE cc_start: 0.8041 (m-10) cc_final: 0.7649 (m-80) REVERT: A 441 ASP cc_start: 0.8561 (p0) cc_final: 0.8244 (p0) REVERT: A 442 ASP cc_start: 0.8701 (m-30) cc_final: 0.8439 (m-30) outliers start: 4 outliers final: 3 residues processed: 39 average time/residue: 0.0739 time to fit residues: 3.6508 Evaluate side-chains 36 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.0670 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.111769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.084010 restraints weight = 5683.562| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.31 r_work: 0.2983 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3458 Z= 0.133 Angle : 0.558 7.703 4687 Z= 0.276 Chirality : 0.040 0.207 535 Planarity : 0.004 0.062 555 Dihedral : 11.003 94.771 533 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.12 % Allowed : 14.85 % Favored : 84.03 % 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: 2.03 (0.46), residues: 396 helix: 3.64 (0.36), residues: 206 sheet: 0.74 (0.66), residues: 63 loop : -2.56 (0.49), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.014 0.001 TYR A 83 PHE 0.012 0.001 PHE A 55 TRP 0.007 0.001 TRP A 82 HIS 0.002 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3454) covalent geometry : angle 0.53630 ( 4677) SS BOND : bond 0.00508 ( 2) SS BOND : angle 1.21084 ( 4) hydrogen bonds : bond 0.04806 ( 197) hydrogen bonds : angle 3.18454 ( 576) link_NAG-ASN : bond 0.00532 ( 2) link_NAG-ASN : angle 4.29434 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 795.63 seconds wall clock time: 14 minutes 19.07 seconds (859.07 seconds total)