Starting phenix.real_space_refine on Thu Mar 6 01:39:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y7z_33675/03_2025/7y7z_33675.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y7z_33675/03_2025/7y7z_33675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y7z_33675/03_2025/7y7z_33675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y7z_33675/03_2025/7y7z_33675.map" model { file = "/net/cci-nas-00/data/ceres_data/7y7z_33675/03_2025/7y7z_33675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y7z_33675/03_2025/7y7z_33675.cif" } resolution = 3.2 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= 0.002 sd= 0.130 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 S 36 5.16 5 Cl 1 4.86 5 C 2876 2.51 5 N 661 2.21 5 O 729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4303 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4235 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 23, 'TRANS': 508} Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 68 Unusual residues: {' CL': 1, 'NAG': 3, 'TGI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.88, per 1000 atoms: 0.67 Number of scatterers: 4303 At special positions: 0 Unit cell: (71.445, 74.6925, 96.3425, 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) Cl 1 17.00 S 36 16.00 O 729 8.00 N 661 7.00 C 2876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 173 " distance=2.02 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 702 " - " ASN A 181 " " NAG A 703 " - " ASN A 176 " " NAG A 704 " - " ASN A 184 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 494.7 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 77.4% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 49 through 60 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.643A pdb=" N VAL A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 94 through 109 Processing helix chain 'A' and resid 119 through 122 Processing helix chain 'A' and resid 123 through 155 removed outlier: 3.764A pdb=" N LEU A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 211 through 230 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.946A pdb=" N GLY A 237 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 260 removed outlier: 3.895A pdb=" N THR A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.660A pdb=" N GLY A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.901A pdb=" N TRP A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 310 removed outlier: 4.157A pdb=" N ALA A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 350 removed outlier: 3.518A pdb=" N GLY A 343 " --> pdb=" O PHE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 363 through 374 removed outlier: 3.511A pdb=" N TYR A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 377 through 412 removed outlier: 3.668A pdb=" N TRP A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 419 through 439 Processing helix chain 'A' and resid 442 through 454 removed outlier: 4.315A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 474 removed outlier: 3.676A pdb=" N PHE A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 Processing helix chain 'A' and resid 493 through 519 removed outlier: 4.511A pdb=" N LYS A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N THR A 504 " --> pdb=" O TRP A 500 " (cutoff:3.500A) Proline residue: A 505 - end of helix removed outlier: 3.527A pdb=" N GLN A 518 " --> pdb=" O PHE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 546 Processing helix chain 'A' and resid 546 through 559 removed outlier: 3.749A pdb=" N LEU A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 572 Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 174 removed outlier: 3.565A pdb=" N PHE A 174 " --> pdb=" O THR A 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 523 through 524 282 hydrogen bonds defined for protein. 837 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: 1.05 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 648 1.32 - 1.45: 1359 1.45 - 1.57: 2375 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 4440 Sorted by residual: bond pdb=" C17 TGI A 701 " pdb=" O19 TGI A 701 " ideal model delta sigma weight residual 1.261 1.203 0.058 2.00e-02 2.50e+03 8.37e+00 bond pdb=" C20 TGI A 701 " pdb=" C21 TGI A 701 " ideal model delta sigma weight residual 1.374 1.430 -0.056 2.00e-02 2.50e+03 7.91e+00 bond pdb=" C17 TGI A 701 " pdb=" O18 TGI A 701 " ideal model delta sigma weight residual 1.260 1.204 0.056 2.00e-02 2.50e+03 7.80e+00 bond pdb=" N VAL A 323 " pdb=" CA VAL A 323 " ideal model delta sigma weight residual 1.461 1.492 -0.030 1.17e-02 7.31e+03 6.73e+00 bond pdb=" C02 TGI A 701 " pdb=" C03 TGI A 701 " ideal model delta sigma weight residual 1.380 1.423 -0.043 2.00e-02 2.50e+03 4.57e+00 ... (remaining 4435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 5561 1.15 - 2.30: 382 2.30 - 3.45: 71 3.45 - 4.59: 27 4.59 - 5.74: 8 Bond angle restraints: 6049 Sorted by residual: angle pdb=" CA TYR A 60 " pdb=" CB TYR A 60 " pdb=" CG TYR A 60 " ideal model delta sigma weight residual 113.90 119.64 -5.74 1.80e+00 3.09e-01 1.02e+01 angle pdb=" C ILE A 138 " pdb=" N TYR A 139 " pdb=" CA TYR A 139 " ideal model delta sigma weight residual 121.14 115.83 5.31 1.75e+00 3.27e-01 9.22e+00 angle pdb=" CA VAL A 323 " pdb=" C VAL A 323 " pdb=" O VAL A 323 " ideal model delta sigma weight residual 121.17 118.28 2.89 1.06e+00 8.90e-01 7.43e+00 angle pdb=" O VAL A 323 " pdb=" C VAL A 323 " pdb=" N CYS A 324 " ideal model delta sigma weight residual 121.91 124.44 -2.53 9.80e-01 1.04e+00 6.67e+00 angle pdb=" CA TYR A 139 " pdb=" CB TYR A 139 " pdb=" CG TYR A 139 " ideal model delta sigma weight residual 113.90 118.46 -4.56 1.80e+00 3.09e-01 6.41e+00 ... (remaining 6044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.49: 2287 20.49 - 40.98: 252 40.98 - 61.47: 16 61.47 - 81.96: 2 81.96 - 102.45: 2 Dihedral angle restraints: 2559 sinusoidal: 1027 harmonic: 1532 Sorted by residual: dihedral pdb=" CA SER A 456 " pdb=" C SER A 456 " pdb=" N GLY A 457 " pdb=" CA GLY A 457 " ideal model delta harmonic sigma weight residual -180.00 -157.18 -22.82 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA PHE A 339 " pdb=" C PHE A 339 " pdb=" N SER A 340 " pdb=" CA SER A 340 " ideal model delta harmonic sigma weight residual 180.00 158.37 21.63 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA TRP A 116 " pdb=" C TRP A 116 " pdb=" N LYS A 117 " pdb=" CA LYS A 117 " ideal model delta harmonic sigma weight residual 180.00 158.74 21.26 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 2556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 512 0.049 - 0.099: 129 0.099 - 0.148: 27 0.148 - 0.198: 2 0.198 - 0.247: 1 Chirality restraints: 671 Sorted by residual: chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 176 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA VAL A 323 " pdb=" N VAL A 323 " pdb=" C VAL A 323 " pdb=" CB VAL A 323 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 181 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 668 not shown) Planarity restraints: 736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 184 " 0.219 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" CG ASN A 184 " -0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN A 184 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 184 " -0.483 2.00e-02 2.50e+03 pdb=" C1 NAG A 704 " 0.333 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C03 TGI A 701 " 0.009 2.00e-02 2.50e+03 1.80e-01 4.05e+02 pdb=" C07 TGI A 701 " 0.042 2.00e-02 2.50e+03 pdb=" C08 TGI A 701 " 0.307 2.00e-02 2.50e+03 pdb=" C09 TGI A 701 " -0.210 2.00e-02 2.50e+03 pdb=" C20 TGI A 701 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 176 " -0.099 2.00e-02 2.50e+03 1.58e-01 3.11e+02 pdb=" CG ASN A 176 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " -0.055 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " 0.282 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " -0.173 2.00e-02 2.50e+03 ... (remaining 733 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 38 2.61 - 3.18: 4047 3.18 - 3.75: 6585 3.75 - 4.33: 8993 4.33 - 4.90: 15408 Nonbonded interactions: 35071 Sorted by model distance: nonbonded pdb=" OG1 THR A 170 " pdb=" OE2 GLU A 191 " model vdw 2.037 3.040 nonbonded pdb=" O GLY A 561 " pdb=" NH1 ARG A 566 " model vdw 2.119 3.120 nonbonded pdb=" O LEU A 279 " pdb=" OG SER A 280 " model vdw 2.258 3.040 nonbonded pdb=" O GLY A 114 " pdb=" N LYS A 117 " model vdw 2.278 3.120 nonbonded pdb=" OD1 ASN A 181 " pdb=" OG1 THR A 183 " model vdw 2.304 3.040 ... (remaining 35066 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: 0.370 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.270 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 4440 Z= 0.386 Angle : 0.712 5.743 6049 Z= 0.388 Chirality : 0.045 0.247 671 Planarity : 0.009 0.180 733 Dihedral : 15.326 102.447 1584 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.38), residues: 530 helix: 0.55 (0.27), residues: 395 sheet: None (None), residues: 0 loop : -1.79 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 193 HIS 0.002 0.001 HIS A 347 PHE 0.016 0.002 PHE A 512 TYR 0.029 0.002 TYR A 60 ARG 0.003 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.413 Fit side-chains REVERT: A 152 TYR cc_start: 0.8218 (t80) cc_final: 0.7910 (t80) REVERT: A 314 ASN cc_start: 0.8805 (t0) cc_final: 0.8596 (t0) REVERT: A 491 ARG cc_start: 0.8383 (mmm160) cc_final: 0.8061 (ttm170) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1604 time to fit residues: 14.8716 Evaluate side-chains 69 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.172512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132776 restraints weight = 4505.748| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.94 r_work: 0.3066 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4440 Z= 0.232 Angle : 0.687 10.102 6049 Z= 0.342 Chirality : 0.048 0.350 671 Planarity : 0.005 0.040 733 Dihedral : 7.799 88.793 666 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.88 % Allowed : 9.51 % Favored : 89.60 % 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: 0.51 (0.38), residues: 530 helix: 0.96 (0.27), residues: 397 sheet: None (None), residues: 0 loop : -1.46 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 193 HIS 0.002 0.001 HIS A 347 PHE 0.017 0.002 PHE A 385 TYR 0.025 0.002 TYR A 60 ARG 0.004 0.001 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 314 ASN cc_start: 0.8639 (t0) cc_final: 0.8386 (t0) outliers start: 4 outliers final: 3 residues processed: 64 average time/residue: 0.1106 time to fit residues: 10.0266 Evaluate side-chains 62 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 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 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.172842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.133212 restraints weight = 4487.194| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.94 r_work: 0.3072 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4440 Z= 0.224 Angle : 0.642 9.099 6049 Z= 0.319 Chirality : 0.046 0.365 671 Planarity : 0.004 0.040 733 Dihedral : 7.526 87.210 666 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.77 % Allowed : 12.17 % Favored : 86.06 % 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: 0.78 (0.38), residues: 530 helix: 1.22 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -1.48 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 193 HIS 0.002 0.001 HIS A 347 PHE 0.013 0.001 PHE A 51 TYR 0.026 0.002 TYR A 60 ARG 0.002 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.464 Fit side-chains REVERT: A 314 ASN cc_start: 0.8623 (t0) cc_final: 0.8388 (t0) REVERT: A 345 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7183 (mtp) outliers start: 8 outliers final: 4 residues processed: 70 average time/residue: 0.1135 time to fit residues: 11.1674 Evaluate side-chains 69 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.172339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.132737 restraints weight = 4515.530| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.93 r_work: 0.3067 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4440 Z= 0.234 Angle : 0.629 7.238 6049 Z= 0.314 Chirality : 0.046 0.371 671 Planarity : 0.004 0.043 733 Dihedral : 7.538 85.714 666 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.21 % Allowed : 13.94 % Favored : 83.85 % 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: 0.84 (0.38), residues: 530 helix: 1.21 (0.27), residues: 401 sheet: None (None), residues: 0 loop : -1.45 (0.55), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 193 HIS 0.002 0.001 HIS A 347 PHE 0.016 0.001 PHE A 474 TYR 0.027 0.002 TYR A 60 ARG 0.002 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 314 ASN cc_start: 0.8615 (t0) cc_final: 0.8376 (t0) REVERT: A 345 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7157 (mtp) REVERT: A 355 ASP cc_start: 0.8156 (t0) cc_final: 0.7945 (t0) outliers start: 10 outliers final: 6 residues processed: 73 average time/residue: 0.1020 time to fit residues: 10.7864 Evaluate side-chains 70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 48 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 0.0010 chunk 52 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 6 optimal weight: 0.0370 chunk 22 optimal weight: 1.9990 overall best weight: 0.4464 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.176153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.136767 restraints weight = 4565.620| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.96 r_work: 0.3179 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4440 Z= 0.181 Angle : 0.598 6.317 6049 Z= 0.297 Chirality : 0.045 0.363 671 Planarity : 0.004 0.042 733 Dihedral : 7.788 84.088 666 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.21 % Allowed : 16.15 % Favored : 81.64 % 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: 0.89 (0.38), residues: 530 helix: 1.20 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -1.41 (0.56), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 193 HIS 0.001 0.000 HIS A 347 PHE 0.013 0.001 PHE A 474 TYR 0.025 0.001 TYR A 60 ARG 0.002 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.683 Fit side-chains REVERT: A 185 MET cc_start: 0.6821 (OUTLIER) cc_final: 0.5990 (mmm) REVERT: A 314 ASN cc_start: 0.8651 (t0) cc_final: 0.8427 (t0) REVERT: A 355 ASP cc_start: 0.8318 (t0) cc_final: 0.8053 (t0) outliers start: 10 outliers final: 7 residues processed: 69 average time/residue: 0.1218 time to fit residues: 12.3708 Evaluate side-chains 65 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.175583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.136250 restraints weight = 4485.541| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.94 r_work: 0.2903 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4440 Z= 0.193 Angle : 0.606 6.360 6049 Z= 0.301 Chirality : 0.046 0.355 671 Planarity : 0.004 0.044 733 Dihedral : 7.785 82.675 666 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.43 % Allowed : 17.26 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.38), residues: 530 helix: 1.30 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -1.34 (0.57), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 193 HIS 0.001 0.000 HIS A 347 PHE 0.012 0.001 PHE A 474 TYR 0.027 0.001 TYR A 60 ARG 0.001 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 185 MET cc_start: 0.6756 (mtp) cc_final: 0.5931 (mmm) REVERT: A 355 ASP cc_start: 0.8253 (t0) cc_final: 0.8009 (t0) outliers start: 11 outliers final: 9 residues processed: 68 average time/residue: 0.1069 time to fit residues: 10.5057 Evaluate side-chains 65 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 506 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.173797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.134374 restraints weight = 4528.121| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.94 r_work: 0.2878 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4440 Z= 0.216 Angle : 0.616 6.745 6049 Z= 0.306 Chirality : 0.046 0.357 671 Planarity : 0.004 0.044 733 Dihedral : 7.784 82.878 666 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.54 % Allowed : 17.70 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.38), residues: 530 helix: 1.33 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -1.28 (0.59), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 230 HIS 0.001 0.000 HIS A 313 PHE 0.011 0.001 PHE A 294 TYR 0.027 0.001 TYR A 60 ARG 0.001 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.410 Fit side-chains REVERT: A 185 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.6182 (mmm) REVERT: A 355 ASP cc_start: 0.8267 (t0) cc_final: 0.8030 (t0) outliers start: 16 outliers final: 9 residues processed: 70 average time/residue: 0.0996 time to fit residues: 10.0723 Evaluate side-chains 67 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 552 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 0.0770 chunk 44 optimal weight: 0.0970 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 19 optimal weight: 0.0270 chunk 37 optimal weight: 0.9980 chunk 9 optimal weight: 0.0670 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 overall best weight: 0.1732 ------------------------------------------------------------------------------- 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 = 0.4198 r_free = 0.4198 target = 0.181805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.143132 restraints weight = 4433.378| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.93 r_work: 0.3005 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4440 Z= 0.154 Angle : 0.601 7.508 6049 Z= 0.296 Chirality : 0.045 0.389 671 Planarity : 0.004 0.045 733 Dihedral : 7.735 86.898 666 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.43 % Allowed : 17.70 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.38), residues: 530 helix: 1.47 (0.26), residues: 411 sheet: None (None), residues: 0 loop : -1.12 (0.59), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 230 HIS 0.001 0.001 HIS A 347 PHE 0.009 0.001 PHE A 474 TYR 0.026 0.001 TYR A 60 ARG 0.001 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.5866 (tmm) cc_final: 0.4829 (mmt) REVERT: A 185 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.5624 (mmt) REVERT: A 250 MET cc_start: 0.7181 (mmm) cc_final: 0.6921 (mmm) REVERT: A 355 ASP cc_start: 0.8208 (t0) cc_final: 0.7974 (t0) REVERT: A 473 TRP cc_start: 0.8679 (m-10) cc_final: 0.8465 (m-10) outliers start: 11 outliers final: 8 residues processed: 67 average time/residue: 0.1101 time to fit residues: 10.5767 Evaluate side-chains 68 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 506 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.176307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.137062 restraints weight = 4472.879| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.94 r_work: 0.2926 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4440 Z= 0.205 Angle : 0.617 6.859 6049 Z= 0.306 Chirality : 0.045 0.366 671 Planarity : 0.004 0.044 733 Dihedral : 7.732 84.350 666 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.21 % Allowed : 19.47 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.38), residues: 530 helix: 1.46 (0.26), residues: 411 sheet: None (None), residues: 0 loop : -1.18 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 230 HIS 0.004 0.001 HIS A 198 PHE 0.011 0.001 PHE A 294 TYR 0.027 0.001 TYR A 60 ARG 0.001 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.5778 (tmm) cc_final: 0.4877 (mmt) REVERT: A 185 MET cc_start: 0.6023 (mtp) cc_final: 0.5678 (mmt) REVERT: A 355 ASP cc_start: 0.8330 (t0) cc_final: 0.8082 (t0) REVERT: A 473 TRP cc_start: 0.8746 (m-10) cc_final: 0.8537 (m-10) outliers start: 10 outliers final: 9 residues processed: 71 average time/residue: 0.1065 time to fit residues: 10.8486 Evaluate side-chains 72 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 506 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 0.0870 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.175939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.136471 restraints weight = 4451.414| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.95 r_work: 0.2917 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4440 Z= 0.211 Angle : 0.630 8.383 6049 Z= 0.312 Chirality : 0.047 0.367 671 Planarity : 0.004 0.044 733 Dihedral : 7.832 84.607 666 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.21 % Allowed : 19.25 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.38), residues: 530 helix: 1.48 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -1.23 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 230 HIS 0.002 0.001 HIS A 198 PHE 0.011 0.001 PHE A 294 TYR 0.027 0.001 TYR A 60 ARG 0.002 0.000 ARG A 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.5899 (tmm) cc_final: 0.4761 (mmt) REVERT: A 250 MET cc_start: 0.7280 (mmm) cc_final: 0.7001 (mmm) REVERT: A 355 ASP cc_start: 0.8347 (t0) cc_final: 0.8101 (t0) outliers start: 10 outliers final: 10 residues processed: 64 average time/residue: 0.1049 time to fit residues: 9.6925 Evaluate side-chains 67 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 506 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 32 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 25 optimal weight: 0.0070 chunk 30 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.174516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.135148 restraints weight = 4497.396| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.96 r_work: 0.2897 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4440 Z= 0.220 Angle : 0.628 7.931 6049 Z= 0.311 Chirality : 0.046 0.370 671 Planarity : 0.004 0.044 733 Dihedral : 7.838 84.305 666 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.43 % Allowed : 19.03 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.38), residues: 530 helix: 1.49 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -1.22 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 230 HIS 0.002 0.001 HIS A 198 PHE 0.011 0.001 PHE A 294 TYR 0.028 0.001 TYR A 60 ARG 0.001 0.000 ARG A 318 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2804.08 seconds wall clock time: 49 minutes 29.70 seconds (2969.70 seconds total)