Starting phenix.real_space_refine on Wed Jul 23 23:17:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jda_61386/07_2025/9jda_61386_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jda_61386/07_2025/9jda_61386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jda_61386/07_2025/9jda_61386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jda_61386/07_2025/9jda_61386.map" model { file = "/net/cci-nas-00/data/ceres_data/9jda_61386/07_2025/9jda_61386_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jda_61386/07_2025/9jda_61386_neut.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.039 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: 6 Type Number sf(0) Gaussians S 33 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2963 2.51 5 N 668 2.21 5 O 750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4417 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4369 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 28, 'TRANS': 523} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 48 Unusual residues: {' CL': 1, ' NA': 2, 'D10': 1, 'D12': 1, 'OCT': 2, 'TAU': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 3.27, per 1000 atoms: 0.74 Number of scatterers: 4417 At special positions: 0 Unit cell: (83.345, 67.52, 89.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 33 16.00 Na 2 11.00 O 750 8.00 N 668 7.00 C 2963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " 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 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 548.9 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1006 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 1 sheets defined 75.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.524A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.841A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 79 through 106 removed outlier: 6.060A pdb=" N LEU A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 110 through 117 Processing helix chain 'A' and resid 121 through 152 removed outlier: 4.141A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 236 Processing helix chain 'A' and resid 241 through 244 removed outlier: 4.427A pdb=" N LYS A 244 " --> pdb=" O SER A 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 244' Processing helix chain 'A' and resid 245 through 266 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.607A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.503A pdb=" N GLU A 286 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.232A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 321 through 356 removed outlier: 4.219A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 369 through 381 removed outlier: 3.585A pdb=" N TYR A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Proline residue: A 375 - end of helix removed outlier: 3.721A pdb=" N THR A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 416 removed outlier: 3.610A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 445 removed outlier: 4.108A pdb=" N GLU A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.840A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.553A pdb=" N ASP A 490 " --> pdb=" O ASP A 486 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 510 through 526 removed outlier: 3.610A pdb=" N LEU A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 removed outlier: 4.015A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 580 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 277 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1092 1.33 - 1.45: 985 1.45 - 1.57: 2428 1.57 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 4552 Sorted by residual: bond pdb=" N VAL A 195 " pdb=" CA VAL A 195 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.19e-02 7.06e+03 7.71e+00 bond pdb=" N ILE A 196 " pdb=" CA ILE A 196 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.25e+00 bond pdb=" N VAL A 590 " pdb=" CA VAL A 590 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.14e-02 7.69e+03 7.17e+00 bond pdb=" N GLU A 591 " pdb=" CA GLU A 591 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.16e+00 bond pdb=" N ARG A 201 " pdb=" CA ARG A 201 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.32e-02 5.74e+03 5.73e+00 ... (remaining 4547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 6096 2.01 - 4.02: 85 4.02 - 6.03: 11 6.03 - 8.04: 1 8.04 - 10.05: 2 Bond angle restraints: 6195 Sorted by residual: angle pdb=" CA ARG A 587 " pdb=" C ARG A 587 " pdb=" O ARG A 587 " ideal model delta sigma weight residual 122.38 117.90 4.48 1.49e+00 4.50e-01 9.04e+00 angle pdb=" CA VAL A 590 " pdb=" C VAL A 590 " pdb=" O VAL A 590 " ideal model delta sigma weight residual 121.27 118.19 3.08 1.04e+00 9.25e-01 8.79e+00 angle pdb=" CA TRP A 199 " pdb=" C TRP A 199 " pdb=" O TRP A 199 " ideal model delta sigma weight residual 120.82 117.90 2.92 1.05e+00 9.07e-01 7.72e+00 angle pdb=" C VAL A 136 " pdb=" N TYR A 137 " pdb=" CA TYR A 137 " ideal model delta sigma weight residual 122.26 117.61 4.65 1.73e+00 3.34e-01 7.23e+00 angle pdb=" CA ASN A 586 " pdb=" C ASN A 586 " pdb=" O ASN A 586 " ideal model delta sigma weight residual 122.38 118.39 3.99 1.49e+00 4.50e-01 7.18e+00 ... (remaining 6190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.05: 2253 14.05 - 28.10: 237 28.10 - 42.15: 76 42.15 - 56.20: 8 56.20 - 70.25: 5 Dihedral angle restraints: 2579 sinusoidal: 991 harmonic: 1588 Sorted by residual: dihedral pdb=" CA GLU A 200 " pdb=" C GLU A 200 " pdb=" N ARG A 201 " pdb=" CA ARG A 201 " ideal model delta harmonic sigma weight residual -180.00 -157.74 -22.26 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA MET A 172 " pdb=" C MET A 172 " pdb=" N GLU A 173 " pdb=" CA GLU A 173 " ideal model delta harmonic sigma weight residual -180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA SER A 205 " pdb=" C SER A 205 " pdb=" N LEU A 206 " pdb=" CA LEU A 206 " ideal model delta harmonic sigma weight residual -180.00 -164.99 -15.01 0 5.00e+00 4.00e-02 9.01e+00 ... (remaining 2576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 458 0.038 - 0.077: 165 0.077 - 0.115: 47 0.115 - 0.153: 6 0.153 - 0.191: 3 Chirality restraints: 679 Sorted by residual: chirality pdb=" CA VAL A 590 " pdb=" N VAL A 590 " pdb=" C VAL A 590 " pdb=" CB VAL A 590 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.15e-01 chirality pdb=" CA ILE A 196 " pdb=" N ILE A 196 " pdb=" C ILE A 196 " pdb=" CB ILE A 196 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CA THR A 596 " pdb=" N THR A 596 " pdb=" C THR A 596 " pdb=" CB THR A 596 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 676 not shown) Planarity restraints: 753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 201 " -0.212 9.50e-02 1.11e+02 9.50e-02 5.53e+00 pdb=" NE ARG A 201 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 201 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 201 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 201 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 207 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO A 208 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 87 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" C LEU A 87 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU A 87 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE A 88 " 0.011 2.00e-02 2.50e+03 ... (remaining 750 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 68 2.68 - 3.24: 4608 3.24 - 3.79: 7117 3.79 - 4.35: 9980 4.35 - 4.90: 16163 Nonbonded interactions: 37936 Sorted by model distance: nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.130 3.040 nonbonded pdb=" O TYR A 247 " pdb=" OG1 THR A 251 " model vdw 2.203 3.040 nonbonded pdb=" O PHE A 342 " pdb=" OG SER A 346 " model vdw 2.245 3.040 nonbonded pdb=" OG SER A 301 " pdb="NA NA A 707 " model vdw 2.249 2.470 nonbonded pdb=" O2 TAU A 701 " pdb="NA NA A 707 " model vdw 2.253 2.470 ... (remaining 37931 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: 1.020 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.670 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 0.036 4553 Z= 0.222 Angle : 0.607 10.054 6197 Z= 0.343 Chirality : 0.043 0.191 679 Planarity : 0.006 0.095 753 Dihedral : 12.991 70.253 1570 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.34), residues: 548 helix: 0.19 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -1.22 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 236 HIS 0.006 0.002 HIS A 212 PHE 0.022 0.002 PHE A 58 TYR 0.025 0.001 TYR A 148 ARG 0.003 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.22768 ( 277) hydrogen bonds : angle 8.04031 ( 816) SS BOND : bond 0.00504 ( 1) SS BOND : angle 1.17283 ( 2) covalent geometry : bond 0.00438 ( 4552) covalent geometry : angle 0.60686 ( 6195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.476 Fit side-chains REVERT: A 191 PHE cc_start: 0.7743 (m-10) cc_final: 0.7420 (m-80) REVERT: A 287 ASP cc_start: 0.8628 (t0) cc_final: 0.8326 (t0) REVERT: A 289 GLN cc_start: 0.7982 (tp40) cc_final: 0.7381 (pt0) REVERT: A 293 ASP cc_start: 0.8593 (m-30) cc_final: 0.8333 (m-30) REVERT: A 452 MET cc_start: 0.8885 (tpt) cc_final: 0.8543 (tpt) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1548 time to fit residues: 17.1977 Evaluate side-chains 72 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 16 optimal weight: 0.0060 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 74 ASN A 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.148969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.113856 restraints weight = 5561.399| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.93 r_work: 0.2983 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4553 Z= 0.153 Angle : 0.572 9.413 6197 Z= 0.293 Chirality : 0.041 0.185 679 Planarity : 0.005 0.050 753 Dihedral : 5.632 47.707 625 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.29 % Allowed : 6.65 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.35), residues: 548 helix: 0.98 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -1.23 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 470 HIS 0.003 0.001 HIS A 212 PHE 0.024 0.002 PHE A 58 TYR 0.014 0.002 TYR A 489 ARG 0.004 0.001 ARG A 575 Details of bonding type rmsd hydrogen bonds : bond 0.04761 ( 277) hydrogen bonds : angle 5.15315 ( 816) SS BOND : bond 0.00343 ( 1) SS BOND : angle 1.45172 ( 2) covalent geometry : bond 0.00345 ( 4552) covalent geometry : angle 0.57102 ( 6195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8205 (ppp) cc_final: 0.7979 (ppp) REVERT: A 287 ASP cc_start: 0.8641 (t0) cc_final: 0.8411 (t0) REVERT: A 289 GLN cc_start: 0.8231 (tp40) cc_final: 0.7551 (pt0) REVERT: A 293 ASP cc_start: 0.8630 (m-30) cc_final: 0.8343 (m-30) REVERT: A 351 MET cc_start: 0.8833 (mtp) cc_final: 0.8294 (mtp) REVERT: A 421 PHE cc_start: 0.7831 (t80) cc_final: 0.7577 (t80) REVERT: A 452 MET cc_start: 0.8938 (tpt) cc_final: 0.8507 (tpt) REVERT: A 563 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8389 (mp) outliers start: 6 outliers final: 5 residues processed: 80 average time/residue: 0.1337 time to fit residues: 14.1880 Evaluate side-chains 71 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 563 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 chunk 5 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN A 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.148688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.113847 restraints weight = 5530.040| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.92 r_work: 0.2990 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4553 Z= 0.144 Angle : 0.540 9.221 6197 Z= 0.274 Chirality : 0.040 0.189 679 Planarity : 0.004 0.052 753 Dihedral : 5.422 40.771 625 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.72 % Allowed : 8.37 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.35), residues: 548 helix: 1.16 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -1.30 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 PHE 0.028 0.002 PHE A 58 TYR 0.016 0.001 TYR A 69 ARG 0.002 0.000 ARG A 575 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 277) hydrogen bonds : angle 4.78252 ( 816) SS BOND : bond 0.00387 ( 1) SS BOND : angle 1.12527 ( 2) covalent geometry : bond 0.00334 ( 4552) covalent geometry : angle 0.54003 ( 6195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 206 LEU cc_start: 0.8845 (tp) cc_final: 0.8613 (tp) REVERT: A 289 GLN cc_start: 0.8296 (tp40) cc_final: 0.7496 (tt0) REVERT: A 293 ASP cc_start: 0.8626 (m-30) cc_final: 0.8329 (m-30) REVERT: A 421 PHE cc_start: 0.7883 (t80) cc_final: 0.7529 (t80) REVERT: A 452 MET cc_start: 0.9028 (tpt) cc_final: 0.8618 (tpt) REVERT: A 596 THR cc_start: 0.7230 (OUTLIER) cc_final: 0.6857 (m) outliers start: 8 outliers final: 4 residues processed: 80 average time/residue: 0.1577 time to fit residues: 16.5267 Evaluate side-chains 74 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 8 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.148170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.113357 restraints weight = 5563.242| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.92 r_work: 0.2976 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4553 Z= 0.156 Angle : 0.547 9.335 6197 Z= 0.277 Chirality : 0.040 0.185 679 Planarity : 0.004 0.053 753 Dihedral : 5.325 41.669 625 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.50 % Allowed : 10.73 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.35), residues: 548 helix: 1.26 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -1.30 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 PHE 0.028 0.002 PHE A 58 TYR 0.016 0.001 TYR A 69 ARG 0.002 0.000 ARG A 575 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 277) hydrogen bonds : angle 4.71487 ( 816) SS BOND : bond 0.00332 ( 1) SS BOND : angle 1.19797 ( 2) covalent geometry : bond 0.00370 ( 4552) covalent geometry : angle 0.54661 ( 6195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 206 LEU cc_start: 0.8813 (tp) cc_final: 0.8512 (tp) REVERT: A 289 GLN cc_start: 0.8419 (tp40) cc_final: 0.7511 (tt0) REVERT: A 293 ASP cc_start: 0.8684 (m-30) cc_final: 0.8377 (m-30) REVERT: A 421 PHE cc_start: 0.7935 (t80) cc_final: 0.7552 (t80) REVERT: A 452 MET cc_start: 0.9094 (tpt) cc_final: 0.8682 (tpt) REVERT: A 596 THR cc_start: 0.7274 (OUTLIER) cc_final: 0.6942 (m) outliers start: 7 outliers final: 6 residues processed: 81 average time/residue: 0.1384 time to fit residues: 14.9742 Evaluate side-chains 75 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 53 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 49 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.0020 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN A 212 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.152187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.117392 restraints weight = 5622.969| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.96 r_work: 0.3012 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4553 Z= 0.122 Angle : 0.539 9.254 6197 Z= 0.269 Chirality : 0.039 0.183 679 Planarity : 0.004 0.052 753 Dihedral : 5.061 38.956 625 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.15 % Allowed : 10.30 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.35), residues: 548 helix: 1.42 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -1.26 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.005 0.001 HIS A 212 PHE 0.026 0.002 PHE A 58 TYR 0.017 0.001 TYR A 489 ARG 0.002 0.000 ARG A 428 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 277) hydrogen bonds : angle 4.57460 ( 816) SS BOND : bond 0.00256 ( 1) SS BOND : angle 0.98453 ( 2) covalent geometry : bond 0.00276 ( 4552) covalent geometry : angle 0.53836 ( 6195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.9363 (OUTLIER) cc_final: 0.8308 (p90) REVERT: A 206 LEU cc_start: 0.8789 (tp) cc_final: 0.8535 (tp) REVERT: A 234 CYS cc_start: 0.8017 (m) cc_final: 0.7749 (m) REVERT: A 289 GLN cc_start: 0.8413 (tp40) cc_final: 0.7583 (tt0) REVERT: A 293 ASP cc_start: 0.8640 (m-30) cc_final: 0.8333 (m-30) REVERT: A 351 MET cc_start: 0.8919 (mtp) cc_final: 0.8395 (mtp) REVERT: A 421 PHE cc_start: 0.7919 (t80) cc_final: 0.7531 (t80) REVERT: A 429 GLU cc_start: 0.8117 (mp0) cc_final: 0.7758 (pm20) REVERT: A 452 MET cc_start: 0.9063 (tpt) cc_final: 0.8688 (tpt) REVERT: A 564 ARG cc_start: 0.8364 (mmt90) cc_final: 0.8112 (mmt180) REVERT: A 596 THR cc_start: 0.7208 (OUTLIER) cc_final: 0.6854 (m) outliers start: 10 outliers final: 7 residues processed: 84 average time/residue: 0.1415 time to fit residues: 15.7213 Evaluate side-chains 82 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 2 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN A 212 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.150168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.115499 restraints weight = 5588.271| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.93 r_work: 0.2994 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4553 Z= 0.164 Angle : 0.552 9.323 6197 Z= 0.278 Chirality : 0.041 0.188 679 Planarity : 0.004 0.051 753 Dihedral : 5.161 39.607 625 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.15 % Allowed : 11.59 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.35), residues: 548 helix: 1.38 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -1.28 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 470 HIS 0.007 0.001 HIS A 212 PHE 0.028 0.002 PHE A 58 TYR 0.018 0.001 TYR A 69 ARG 0.001 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 277) hydrogen bonds : angle 4.64944 ( 816) SS BOND : bond 0.00353 ( 1) SS BOND : angle 0.85057 ( 2) covalent geometry : bond 0.00392 ( 4552) covalent geometry : angle 0.55150 ( 6195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.491 Fit side-chains REVERT: A 69 TYR cc_start: 0.9390 (OUTLIER) cc_final: 0.8430 (p90) REVERT: A 125 TYR cc_start: 0.9115 (m-80) cc_final: 0.8729 (m-80) REVERT: A 141 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.9069 (mp) REVERT: A 191 PHE cc_start: 0.7923 (m-10) cc_final: 0.7618 (m-10) REVERT: A 206 LEU cc_start: 0.8794 (tp) cc_final: 0.8499 (tp) REVERT: A 219 ASP cc_start: 0.8540 (p0) cc_final: 0.8284 (p0) REVERT: A 234 CYS cc_start: 0.8055 (m) cc_final: 0.7763 (m) REVERT: A 289 GLN cc_start: 0.8349 (tp40) cc_final: 0.7527 (pt0) REVERT: A 293 ASP cc_start: 0.8614 (m-30) cc_final: 0.8313 (m-30) REVERT: A 421 PHE cc_start: 0.7967 (t80) cc_final: 0.7592 (t80) REVERT: A 429 GLU cc_start: 0.8168 (mp0) cc_final: 0.7799 (pm20) REVERT: A 452 MET cc_start: 0.9117 (tpt) cc_final: 0.8692 (tpt) REVERT: A 564 ARG cc_start: 0.8375 (mmt90) cc_final: 0.8164 (mmt180) REVERT: A 596 THR cc_start: 0.7242 (OUTLIER) cc_final: 0.6904 (m) outliers start: 10 outliers final: 6 residues processed: 83 average time/residue: 0.1486 time to fit residues: 16.3768 Evaluate side-chains 81 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 33 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 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 151 GLN A 212 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.150533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.115793 restraints weight = 5604.937| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.94 r_work: 0.2998 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4553 Z= 0.146 Angle : 0.540 9.301 6197 Z= 0.272 Chirality : 0.040 0.192 679 Planarity : 0.004 0.052 753 Dihedral : 5.117 38.563 625 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.58 % Allowed : 11.16 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.35), residues: 548 helix: 1.43 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -1.29 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 470 HIS 0.007 0.001 HIS A 212 PHE 0.029 0.002 PHE A 58 TYR 0.017 0.001 TYR A 489 ARG 0.002 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 277) hydrogen bonds : angle 4.58468 ( 816) SS BOND : bond 0.00267 ( 1) SS BOND : angle 0.99781 ( 2) covalent geometry : bond 0.00343 ( 4552) covalent geometry : angle 0.54005 ( 6195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.476 Fit side-chains REVERT: A 69 TYR cc_start: 0.9356 (OUTLIER) cc_final: 0.8459 (p90) REVERT: A 191 PHE cc_start: 0.7791 (m-10) cc_final: 0.7536 (m-10) REVERT: A 219 ASP cc_start: 0.8550 (p0) cc_final: 0.8285 (p0) REVERT: A 289 GLN cc_start: 0.8386 (tp40) cc_final: 0.7496 (pt0) REVERT: A 293 ASP cc_start: 0.8629 (m-30) cc_final: 0.8319 (m-30) REVERT: A 421 PHE cc_start: 0.7985 (t80) cc_final: 0.7613 (t80) REVERT: A 429 GLU cc_start: 0.8216 (mp0) cc_final: 0.7937 (pm20) REVERT: A 452 MET cc_start: 0.9118 (tpt) cc_final: 0.8739 (tpt) REVERT: A 596 THR cc_start: 0.7269 (OUTLIER) cc_final: 0.7047 (m) outliers start: 12 outliers final: 7 residues processed: 87 average time/residue: 0.1475 time to fit residues: 16.8505 Evaluate side-chains 79 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS A 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.151901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.117442 restraints weight = 5571.239| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.92 r_work: 0.3009 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4553 Z= 0.146 Angle : 0.554 10.191 6197 Z= 0.278 Chirality : 0.040 0.186 679 Planarity : 0.004 0.051 753 Dihedral : 5.081 37.696 625 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.36 % Allowed : 12.02 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.35), residues: 548 helix: 1.44 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -1.25 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 470 HIS 0.008 0.002 HIS A 212 PHE 0.029 0.002 PHE A 58 TYR 0.019 0.001 TYR A 489 ARG 0.002 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 277) hydrogen bonds : angle 4.58446 ( 816) SS BOND : bond 0.00257 ( 1) SS BOND : angle 1.18008 ( 2) covalent geometry : bond 0.00343 ( 4552) covalent geometry : angle 0.55393 ( 6195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.463 Fit side-chains REVERT: A 69 TYR cc_start: 0.9349 (OUTLIER) cc_final: 0.8486 (p90) REVERT: A 219 ASP cc_start: 0.8569 (p0) cc_final: 0.8302 (p0) REVERT: A 289 GLN cc_start: 0.8372 (tp40) cc_final: 0.7389 (tt0) REVERT: A 293 ASP cc_start: 0.8623 (m-30) cc_final: 0.8355 (m-30) REVERT: A 421 PHE cc_start: 0.7973 (t80) cc_final: 0.7618 (t80) REVERT: A 452 MET cc_start: 0.9130 (tpt) cc_final: 0.8726 (tpt) REVERT: A 596 THR cc_start: 0.7429 (OUTLIER) cc_final: 0.7127 (m) outliers start: 11 outliers final: 7 residues processed: 84 average time/residue: 0.1404 time to fit residues: 15.6568 Evaluate side-chains 81 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 0.0980 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.151951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.117637 restraints weight = 5639.231| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.92 r_work: 0.2984 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4553 Z= 0.151 Angle : 0.581 11.594 6197 Z= 0.286 Chirality : 0.041 0.186 679 Planarity : 0.004 0.051 753 Dihedral : 5.127 37.246 625 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.36 % Allowed : 12.45 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.35), residues: 548 helix: 1.41 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -1.30 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 470 HIS 0.011 0.002 HIS A 212 PHE 0.030 0.002 PHE A 58 TYR 0.020 0.001 TYR A 489 ARG 0.002 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 277) hydrogen bonds : angle 4.59111 ( 816) SS BOND : bond 0.00266 ( 1) SS BOND : angle 1.54148 ( 2) covalent geometry : bond 0.00358 ( 4552) covalent geometry : angle 0.58076 ( 6195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.444 Fit side-chains REVERT: A 69 TYR cc_start: 0.9333 (OUTLIER) cc_final: 0.8485 (p90) REVERT: A 206 LEU cc_start: 0.8840 (tp) cc_final: 0.8597 (tp) REVERT: A 219 ASP cc_start: 0.8560 (p0) cc_final: 0.8293 (p0) REVERT: A 289 GLN cc_start: 0.8397 (tp40) cc_final: 0.7405 (tt0) REVERT: A 293 ASP cc_start: 0.8629 (m-30) cc_final: 0.8361 (m-30) REVERT: A 421 PHE cc_start: 0.7985 (t80) cc_final: 0.7625 (t80) REVERT: A 452 MET cc_start: 0.9137 (tpt) cc_final: 0.8727 (tpt) REVERT: A 596 THR cc_start: 0.7439 (OUTLIER) cc_final: 0.7136 (m) outliers start: 11 outliers final: 7 residues processed: 83 average time/residue: 0.1314 time to fit residues: 14.7735 Evaluate side-chains 83 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 35 optimal weight: 0.2980 chunk 20 optimal weight: 0.0870 chunk 3 optimal weight: 0.4980 chunk 31 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.151910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.117864 restraints weight = 5554.590| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.91 r_work: 0.3022 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4553 Z= 0.118 Angle : 0.573 10.771 6197 Z= 0.284 Chirality : 0.040 0.183 679 Planarity : 0.004 0.050 753 Dihedral : 4.967 33.179 625 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.36 % Allowed : 13.30 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.36), residues: 548 helix: 1.49 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.36 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.011 0.002 HIS A 212 PHE 0.027 0.001 PHE A 58 TYR 0.019 0.001 TYR A 489 ARG 0.002 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 277) hydrogen bonds : angle 4.50589 ( 816) SS BOND : bond 0.00446 ( 1) SS BOND : angle 1.44519 ( 2) covalent geometry : bond 0.00265 ( 4552) covalent geometry : angle 0.57255 ( 6195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.487 Fit side-chains REVERT: A 69 TYR cc_start: 0.9277 (OUTLIER) cc_final: 0.8459 (p90) REVERT: A 172 MET cc_start: 0.6637 (pmm) cc_final: 0.6168 (pmm) REVERT: A 191 PHE cc_start: 0.7139 (m-80) cc_final: 0.6438 (t80) REVERT: A 206 LEU cc_start: 0.8810 (tp) cc_final: 0.8569 (tp) REVERT: A 219 ASP cc_start: 0.8554 (p0) cc_final: 0.8270 (p0) REVERT: A 289 GLN cc_start: 0.8394 (tp40) cc_final: 0.7359 (tt0) REVERT: A 293 ASP cc_start: 0.8622 (m-30) cc_final: 0.8332 (m-30) REVERT: A 421 PHE cc_start: 0.7983 (t80) cc_final: 0.7641 (t80) REVERT: A 452 MET cc_start: 0.9112 (tpt) cc_final: 0.8800 (tpt) REVERT: A 596 THR cc_start: 0.7461 (OUTLIER) cc_final: 0.7223 (m) outliers start: 11 outliers final: 8 residues processed: 85 average time/residue: 0.1375 time to fit residues: 15.7860 Evaluate side-chains 84 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 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 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.151615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.117808 restraints weight = 5612.590| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.90 r_work: 0.3024 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4553 Z= 0.149 Angle : 0.591 9.886 6197 Z= 0.296 Chirality : 0.041 0.189 679 Planarity : 0.004 0.051 753 Dihedral : 4.996 32.791 625 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.15 % Allowed : 14.16 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.36), residues: 548 helix: 1.48 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -1.45 (0.43), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 470 HIS 0.015 0.003 HIS A 212 PHE 0.031 0.002 PHE A 58 TYR 0.018 0.001 TYR A 69 ARG 0.004 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 277) hydrogen bonds : angle 4.58843 ( 816) SS BOND : bond 0.00434 ( 1) SS BOND : angle 1.18559 ( 2) covalent geometry : bond 0.00354 ( 4552) covalent geometry : angle 0.59085 ( 6195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2656.59 seconds wall clock time: 46 minutes 24.94 seconds (2784.94 seconds total)