Starting phenix.real_space_refine on Wed Mar 5 18:15:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9boi_44742/03_2025/9boi_44742.cif Found real_map, /net/cci-nas-00/data/ceres_data/9boi_44742/03_2025/9boi_44742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9boi_44742/03_2025/9boi_44742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9boi_44742/03_2025/9boi_44742.map" model { file = "/net/cci-nas-00/data/ceres_data/9boi_44742/03_2025/9boi_44742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9boi_44742/03_2025/9boi_44742.cif" } resolution = 3.22 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= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 13 5.16 5 C 2136 2.51 5 N 539 2.21 5 O 567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 3256 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3221 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 19, 'TRANS': 403} Chain breaks: 2 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'42H': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.77, per 1000 atoms: 0.85 Number of scatterers: 3256 At special positions: 0 Unit cell: (65.682, 70.11, 78.228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 P 1 15.00 O 567 8.00 N 539 7.00 C 2136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.5 seconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 87.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 56 through 78 removed outlier: 4.000A pdb=" N LEU A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) 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 90 Processing helix chain 'A' and resid 94 through 120 removed outlier: 4.167A pdb=" N GLY A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 123 through 143 Processing helix chain 'A' and resid 150 through 179 Proline residue: A 172 - end of helix removed outlier: 3.977A pdb=" N ILE A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 179 " --> pdb=" O ILE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 214 Proline residue: A 196 - end of helix Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 224 through 237 removed outlier: 3.969A pdb=" N VAL A 228 " --> pdb=" O PRO A 224 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 270 through 306 removed outlier: 3.740A pdb=" N VAL A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Proline residue: A 295 - end of helix Processing helix chain 'A' and resid 319 through 349 removed outlier: 4.422A pdb=" N HIS A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 377 removed outlier: 3.883A pdb=" N LEU A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 368 - end of helix removed outlier: 3.670A pdb=" N LEU A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA A 375 " --> pdb=" O PHE A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 397 removed outlier: 3.808A pdb=" N THR A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 394 " --> pdb=" O ILE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 410 removed outlier: 3.538A pdb=" N VAL A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 432 Processing helix chain 'A' and resid 433 through 443 removed outlier: 4.477A pdb=" N GLY A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A 440 " --> pdb=" O TYR A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 497 removed outlier: 3.623A pdb=" N PHE A 484 " --> pdb=" O GLY A 480 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N GLU A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ALA A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 783 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 968 1.34 - 1.45: 496 1.45 - 1.57: 1846 1.57 - 1.69: 0 1.69 - 1.80: 22 Bond restraints: 3332 Sorted by residual: bond pdb=" O3 42H A 801 " pdb=" P 42H A 801 " ideal model delta sigma weight residual 1.647 1.777 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" C2 42H A 801 " pdb=" C3 42H A 801 " ideal model delta sigma weight residual 1.512 1.569 -0.057 2.00e-02 2.50e+03 8.00e+00 bond pdb=" O1 42H A 801 " pdb=" P 42H A 801 " ideal model delta sigma weight residual 1.635 1.690 -0.055 2.00e-02 2.50e+03 7.68e+00 bond pdb=" C2 42H A 801 " pdb=" O3 42H A 801 " ideal model delta sigma weight residual 1.408 1.357 0.051 2.00e-02 2.50e+03 6.51e+00 bond pdb=" C 42H A 801 " pdb=" C7 42H A 801 " ideal model delta sigma weight residual 1.520 1.565 -0.045 2.00e-02 2.50e+03 5.00e+00 ... (remaining 3327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.82: 4491 3.82 - 7.64: 38 7.64 - 11.45: 3 11.45 - 15.27: 1 15.27 - 19.09: 1 Bond angle restraints: 4534 Sorted by residual: angle pdb=" O1 42H A 801 " pdb=" P 42H A 801 " pdb=" O3 42H A 801 " ideal model delta sigma weight residual 92.88 111.97 -19.09 3.00e+00 1.11e-01 4.05e+01 angle pdb=" O3 42H A 801 " pdb=" P 42H A 801 " pdb=" O4 42H A 801 " ideal model delta sigma weight residual 110.13 97.81 12.32 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C VAL A 82 " pdb=" N LEU A 83 " pdb=" CA LEU A 83 " ideal model delta sigma weight residual 120.09 125.15 -5.06 1.25e+00 6.40e-01 1.64e+01 angle pdb=" CA TRP A 135 " pdb=" CB TRP A 135 " pdb=" CG TRP A 135 " ideal model delta sigma weight residual 113.60 120.70 -7.10 1.90e+00 2.77e-01 1.40e+01 angle pdb=" N ALA A 181 " pdb=" CA ALA A 181 " pdb=" C ALA A 181 " ideal model delta sigma weight residual 111.02 115.50 -4.48 1.22e+00 6.72e-01 1.35e+01 ... (remaining 4529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.34: 1846 28.34 - 56.67: 77 56.67 - 85.00: 6 85.00 - 113.34: 3 113.34 - 141.67: 2 Dihedral angle restraints: 1934 sinusoidal: 738 harmonic: 1196 Sorted by residual: dihedral pdb=" CA VAL A 180 " pdb=" C VAL A 180 " pdb=" N ALA A 181 " pdb=" CA ALA A 181 " ideal model delta harmonic sigma weight residual -180.00 -155.37 -24.63 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" O 42H A 801 " pdb=" C 42H A 801 " pdb=" C7 42H A 801 " pdb=" O5 42H A 801 " ideal model delta sinusoidal sigma weight residual 59.01 -159.32 -141.67 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" C1 42H A 801 " pdb=" C 42H A 801 " pdb=" C7 42H A 801 " pdb=" O5 42H A 801 " ideal model delta sinusoidal sigma weight residual -175.17 -37.72 -137.45 1 3.00e+01 1.11e-03 1.85e+01 ... (remaining 1931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 415 0.054 - 0.108: 100 0.108 - 0.163: 10 0.163 - 0.217: 6 0.217 - 0.271: 1 Chirality restraints: 532 Sorted by residual: chirality pdb=" C 42H A 801 " pdb=" O 42H A 801 " pdb=" C1 42H A 801 " pdb=" C7 42H A 801 " both_signs ideal model delta sigma weight residual False -2.30 -2.57 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA THR A 223 " pdb=" N THR A 223 " pdb=" C THR A 223 " pdb=" CB THR A 223 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA TYR A 408 " pdb=" N TYR A 408 " pdb=" C TYR A 408 " pdb=" CB TYR A 408 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.44e-01 ... (remaining 529 not shown) Planarity restraints: 561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 135 " 0.027 2.00e-02 2.50e+03 2.17e-02 1.18e+01 pdb=" CG TRP A 135 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP A 135 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 135 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 135 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 135 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 135 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 135 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 135 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 135 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 411 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO A 412 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 428 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C LEU A 428 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU A 428 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 429 " 0.009 2.00e-02 2.50e+03 ... (remaining 558 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1037 2.84 - 3.35: 3171 3.35 - 3.87: 5515 3.87 - 4.38: 6033 4.38 - 4.90: 10659 Nonbonded interactions: 26415 Sorted by model distance: nonbonded pdb=" OG SER A 143 " pdb=" NE ARG A 221 " model vdw 2.319 3.120 nonbonded pdb=" OD2 ASP A 120 " pdb=" OG1 THR A 417 " model vdw 2.370 3.040 nonbonded pdb=" NH2 ARG A 121 " pdb=" O THR A 258 " model vdw 2.385 3.120 nonbonded pdb=" NH1 ARG A 302 " pdb=" OD2 ASP A 321 " model vdw 2.395 3.120 nonbonded pdb=" OG SER A 380 " pdb=" N ILE A 381 " model vdw 2.421 3.120 ... (remaining 26410 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.610 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 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 0.130 3332 Z= 0.347 Angle : 0.910 19.089 4534 Z= 0.461 Chirality : 0.049 0.271 532 Planarity : 0.006 0.049 561 Dihedral : 16.428 141.675 1170 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % 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: -1.38 (0.37), residues: 417 helix: -0.56 (0.25), residues: 355 sheet: None (None), residues: 0 loop : -2.08 (0.70), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP A 135 HIS 0.002 0.001 HIS A 495 PHE 0.026 0.002 PHE A 191 TYR 0.018 0.002 TYR A 108 ARG 0.002 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.291 Fit side-chains REVERT: A 210 LYS cc_start: 0.8102 (ttpt) cc_final: 0.7686 (tttp) REVERT: A 292 LEU cc_start: 0.8005 (tt) cc_final: 0.7803 (tt) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.2127 time to fit residues: 9.8478 Evaluate side-chains 33 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN A 427 HIS A 493 GLN A 495 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.166054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.125269 restraints weight = 3409.327| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.63 r_work: 0.3245 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3332 Z= 0.221 Angle : 0.608 10.199 4534 Z= 0.317 Chirality : 0.043 0.177 532 Planarity : 0.005 0.043 561 Dihedral : 12.485 98.161 486 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.59 % Allowed : 12.02 % Favored : 87.39 % 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: 1.05 (0.41), residues: 417 helix: 1.02 (0.27), residues: 347 sheet: None (None), residues: 0 loop : -0.60 (0.81), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 135 HIS 0.003 0.001 HIS A 427 PHE 0.021 0.002 PHE A 191 TYR 0.017 0.002 TYR A 408 ARG 0.003 0.000 ARG A 302 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.360 Fit side-chains REVERT: A 75 ASP cc_start: 0.8166 (t0) cc_final: 0.7736 (m-30) REVERT: A 210 LYS cc_start: 0.7992 (ttpt) cc_final: 0.7683 (tttp) REVERT: A 265 ARG cc_start: 0.7152 (ttt180) cc_final: 0.6584 (ttm-80) outliers start: 2 outliers final: 2 residues processed: 37 average time/residue: 0.2359 time to fit residues: 10.3224 Evaluate side-chains 36 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TRP Chi-restraints excluded: chain A residue 341 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.164810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124242 restraints weight = 3382.595| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.63 r_work: 0.3191 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3332 Z= 0.247 Angle : 0.620 12.117 4534 Z= 0.318 Chirality : 0.043 0.177 532 Planarity : 0.005 0.044 561 Dihedral : 11.919 96.117 486 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.47 % Allowed : 14.66 % Favored : 83.87 % 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: 1.77 (0.42), residues: 417 helix: 1.52 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -0.39 (0.82), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 135 HIS 0.002 0.001 HIS A 427 PHE 0.021 0.002 PHE A 191 TYR 0.018 0.002 TYR A 408 ARG 0.003 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.314 Fit side-chains REVERT: A 75 ASP cc_start: 0.8145 (t0) cc_final: 0.7654 (m-30) REVERT: A 210 LYS cc_start: 0.7879 (ttpt) cc_final: 0.7568 (tttp) REVERT: A 265 ARG cc_start: 0.7038 (ttt180) cc_final: 0.6419 (ttm-80) outliers start: 5 outliers final: 3 residues processed: 36 average time/residue: 0.2279 time to fit residues: 9.6559 Evaluate side-chains 34 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TRP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.0050 chunk 20 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.168867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128047 restraints weight = 3402.113| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.66 r_work: 0.3260 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3332 Z= 0.172 Angle : 0.571 10.555 4534 Z= 0.292 Chirality : 0.041 0.167 532 Planarity : 0.004 0.041 561 Dihedral : 11.396 95.941 486 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.88 % Allowed : 16.42 % Favored : 82.70 % 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: 2.38 (0.42), residues: 417 helix: 1.95 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -0.20 (0.82), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 135 HIS 0.002 0.001 HIS A 349 PHE 0.019 0.001 PHE A 191 TYR 0.014 0.002 TYR A 408 ARG 0.002 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.270 Fit side-chains REVERT: A 210 LYS cc_start: 0.7876 (ttpt) cc_final: 0.7563 (tttp) REVERT: A 265 ARG cc_start: 0.6936 (ttt180) cc_final: 0.6437 (ttm-80) REVERT: A 419 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7711 (mt-10) outliers start: 3 outliers final: 3 residues processed: 31 average time/residue: 0.2593 time to fit residues: 9.6423 Evaluate side-chains 33 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TRP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 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 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.165955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.125180 restraints weight = 3410.719| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.64 r_work: 0.3193 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3332 Z= 0.229 Angle : 0.600 11.829 4534 Z= 0.306 Chirality : 0.042 0.175 532 Planarity : 0.004 0.042 561 Dihedral : 11.294 95.474 486 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.05 % Allowed : 17.30 % Favored : 80.65 % 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: 2.56 (0.42), residues: 417 helix: 2.06 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -0.10 (0.82), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 135 HIS 0.002 0.001 HIS A 427 PHE 0.018 0.002 PHE A 191 TYR 0.019 0.002 TYR A 408 ARG 0.001 0.000 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8105 (t0) cc_final: 0.7758 (m-30) REVERT: A 265 ARG cc_start: 0.6859 (ttt180) cc_final: 0.6304 (ttm-80) outliers start: 7 outliers final: 4 residues processed: 33 average time/residue: 0.2266 time to fit residues: 8.9147 Evaluate side-chains 33 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TRP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.0000 chunk 31 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.167878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.126899 restraints weight = 3498.209| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.66 r_work: 0.3221 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3332 Z= 0.190 Angle : 0.570 11.209 4534 Z= 0.292 Chirality : 0.041 0.171 532 Planarity : 0.004 0.041 561 Dihedral : 10.994 94.752 486 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.17 % Allowed : 18.77 % Favored : 80.06 % 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: 2.82 (0.42), residues: 417 helix: 2.22 (0.28), residues: 347 sheet: None (None), residues: 0 loop : 0.13 (0.83), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 135 HIS 0.002 0.001 HIS A 217 PHE 0.017 0.001 PHE A 191 TYR 0.017 0.002 TYR A 408 ARG 0.002 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8121 (t0) cc_final: 0.7841 (m-30) REVERT: A 265 ARG cc_start: 0.6880 (ttt180) cc_final: 0.6354 (ttm-80) REVERT: A 419 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7595 (mt-10) outliers start: 4 outliers final: 4 residues processed: 32 average time/residue: 0.2075 time to fit residues: 8.0779 Evaluate side-chains 34 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TRP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.166270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.125475 restraints weight = 3417.149| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.64 r_work: 0.3209 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3332 Z= 0.219 Angle : 0.587 11.865 4534 Z= 0.301 Chirality : 0.042 0.177 532 Planarity : 0.004 0.041 561 Dihedral : 10.923 93.353 486 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.47 % Allowed : 19.06 % Favored : 79.47 % 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: 2.81 (0.42), residues: 417 helix: 2.19 (0.28), residues: 347 sheet: None (None), residues: 0 loop : 0.26 (0.84), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 135 HIS 0.002 0.001 HIS A 427 PHE 0.017 0.001 PHE A 421 TYR 0.017 0.002 TYR A 408 ARG 0.003 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8119 (t0) cc_final: 0.7829 (m-30) REVERT: A 265 ARG cc_start: 0.6895 (ttt180) cc_final: 0.6354 (ttm-80) REVERT: A 419 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7633 (mt-10) outliers start: 5 outliers final: 4 residues processed: 35 average time/residue: 0.2598 time to fit residues: 11.3544 Evaluate side-chains 36 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TRP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.165910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.125135 restraints weight = 3418.503| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.62 r_work: 0.3209 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3332 Z= 0.234 Angle : 0.598 11.958 4534 Z= 0.305 Chirality : 0.042 0.178 532 Planarity : 0.004 0.041 561 Dihedral : 10.895 92.793 486 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.17 % Allowed : 18.77 % Favored : 80.06 % 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: 2.82 (0.42), residues: 417 helix: 2.19 (0.28), residues: 347 sheet: None (None), residues: 0 loop : 0.35 (0.85), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 135 HIS 0.002 0.001 HIS A 427 PHE 0.018 0.002 PHE A 421 TYR 0.017 0.002 TYR A 408 ARG 0.002 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8136 (t0) cc_final: 0.7849 (m-30) REVERT: A 265 ARG cc_start: 0.6931 (ttt180) cc_final: 0.6393 (ttm-80) REVERT: A 419 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7671 (mt-10) outliers start: 4 outliers final: 4 residues processed: 33 average time/residue: 0.2064 time to fit residues: 8.2148 Evaluate side-chains 35 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TRP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 0.0980 chunk 37 optimal weight: 0.0970 chunk 24 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.169135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.128482 restraints weight = 3417.113| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.64 r_work: 0.3249 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3332 Z= 0.174 Angle : 0.562 10.627 4534 Z= 0.288 Chirality : 0.041 0.171 532 Planarity : 0.004 0.040 561 Dihedral : 10.621 88.536 486 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.17 % Allowed : 20.23 % Favored : 78.59 % 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: 3.07 (0.42), residues: 417 helix: 2.36 (0.28), residues: 347 sheet: None (None), residues: 0 loop : 0.40 (0.86), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 135 HIS 0.001 0.000 HIS A 427 PHE 0.018 0.001 PHE A 421 TYR 0.015 0.002 TYR A 408 ARG 0.002 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8063 (t0) cc_final: 0.7790 (m-30) REVERT: A 265 ARG cc_start: 0.6905 (ttt180) cc_final: 0.6379 (ttm-80) REVERT: A 419 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7689 (mt-10) outliers start: 4 outliers final: 4 residues processed: 31 average time/residue: 0.2220 time to fit residues: 8.3406 Evaluate side-chains 33 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TRP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 38 optimal weight: 0.0020 chunk 29 optimal weight: 0.0980 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 9 optimal weight: 0.0980 chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 28 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 overall best weight: 0.1988 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.173896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.132630 restraints weight = 3367.207| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.65 r_work: 0.3391 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3332 Z= 0.147 Angle : 0.551 10.064 4534 Z= 0.279 Chirality : 0.040 0.166 532 Planarity : 0.004 0.038 561 Dihedral : 10.034 77.658 486 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.17 % Allowed : 19.35 % Favored : 79.47 % 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: 3.17 (0.42), residues: 417 helix: 2.43 (0.28), residues: 349 sheet: None (None), residues: 0 loop : 0.35 (0.87), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 135 HIS 0.001 0.000 HIS A 427 PHE 0.018 0.001 PHE A 191 TYR 0.012 0.002 TYR A 408 ARG 0.002 0.000 ARG A 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.344 Fit side-chains REVERT: A 265 ARG cc_start: 0.7051 (ttt180) cc_final: 0.6739 (ttm-80) outliers start: 4 outliers final: 4 residues processed: 30 average time/residue: 0.1862 time to fit residues: 6.9543 Evaluate side-chains 32 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TRP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 494 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.0010 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 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 = 0.190585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.152002 restraints weight = 3294.174| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.54 r_work: 0.3307 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3332 Z= 0.200 Angle : 0.582 11.088 4534 Z= 0.295 Chirality : 0.042 0.183 532 Planarity : 0.004 0.038 561 Dihedral : 9.848 74.439 486 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.17 % Allowed : 19.94 % Favored : 78.89 % 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: 3.14 (0.42), residues: 417 helix: 2.39 (0.28), residues: 347 sheet: None (None), residues: 0 loop : 0.50 (0.86), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 135 HIS 0.002 0.001 HIS A 427 PHE 0.019 0.001 PHE A 421 TYR 0.016 0.002 TYR A 408 ARG 0.002 0.000 ARG A 491 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2127.89 seconds wall clock time: 37 minutes 35.57 seconds (2255.57 seconds total)