Starting phenix.real_space_refine on Thu Nov 14 06:17:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hff_34719/11_2024/8hff_34719.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hff_34719/11_2024/8hff_34719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hff_34719/11_2024/8hff_34719.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hff_34719/11_2024/8hff_34719.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hff_34719/11_2024/8hff_34719.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hff_34719/11_2024/8hff_34719.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.127 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2953 2.51 5 N 681 2.21 5 O 745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4399 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4373 Classifications: {'peptide': 547} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 1 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Unusual residues: {'LNR': 2} Classifications: {'undetermined': 2, 'water': 2} Link IDs: {None: 3} Time building chain proxies: 2.97, per 1000 atoms: 0.68 Number of scatterers: 4399 At special positions: 0 Unit cell: (70.3625, 69.28, 98.5075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 745 8.00 N 681 7.00 C 2953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 523.8 milliseconds 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1006 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 1 sheets defined 82.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 60 through 74 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.649A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.691A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 255 through 261 removed outlier: 3.639A pdb=" N THR A 258 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS A 261 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 283 removed outlier: 3.817A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 3.906A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.714A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.968A pdb=" N TYR A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 373 Processing helix chain 'A' and resid 385 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.615A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.796A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 497 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.587A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 removed outlier: 3.507A pdb=" N ILE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 604 removed outlier: 4.040A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N HIS A 599 " --> pdb=" O ASN A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.759A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 302 hydrogen bonds defined for protein. 867 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: 1.28 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 649 1.29 - 1.42: 1370 1.42 - 1.55: 2488 1.55 - 1.68: 0 1.68 - 1.81: 31 Bond restraints: 4538 Sorted by residual: bond pdb=" C GLY A 92 " pdb=" O GLY A 92 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.35e-02 5.49e+03 2.98e+01 bond pdb=" C ASN A 89 " pdb=" O ASN A 89 " ideal model delta sigma weight residual 1.232 1.167 0.065 1.36e-02 5.41e+03 2.31e+01 bond pdb=" C GLY A 92 " pdb=" N ALA A 93 " ideal model delta sigma weight residual 1.332 1.268 0.064 1.40e-02 5.10e+03 2.09e+01 bond pdb=" C GLY A 91 " pdb=" O GLY A 91 " ideal model delta sigma weight residual 1.235 1.186 0.048 1.35e-02 5.49e+03 1.28e+01 bond pdb=" C GLY A 90 " pdb=" O GLY A 90 " ideal model delta sigma weight residual 1.235 1.191 0.043 1.35e-02 5.49e+03 1.03e+01 ... (remaining 4533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 6006 1.31 - 2.61: 131 2.61 - 3.92: 40 3.92 - 5.22: 12 5.22 - 6.53: 1 Bond angle restraints: 6190 Sorted by residual: angle pdb=" CA ASN A 89 " pdb=" C ASN A 89 " pdb=" O ASN A 89 " ideal model delta sigma weight residual 121.17 117.39 3.78 1.24e+00 6.50e-01 9.29e+00 angle pdb=" N GLY A 90 " pdb=" CA GLY A 90 " pdb=" C GLY A 90 " ideal model delta sigma weight residual 113.18 119.71 -6.53 2.37e+00 1.78e-01 7.59e+00 angle pdb=" C ASN A 89 " pdb=" CA ASN A 89 " pdb=" CB ASN A 89 " ideal model delta sigma weight residual 111.23 115.90 -4.67 1.70e+00 3.46e-01 7.53e+00 angle pdb=" C PHE A 150 " pdb=" N TYR A 151 " pdb=" CA TYR A 151 " ideal model delta sigma weight residual 121.14 116.53 4.61 1.75e+00 3.27e-01 6.93e+00 angle pdb=" CA TYR A 151 " pdb=" CB TYR A 151 " pdb=" CG TYR A 151 " ideal model delta sigma weight residual 113.90 118.52 -4.62 1.80e+00 3.09e-01 6.59e+00 ... (remaining 6185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 2209 17.79 - 35.58: 251 35.58 - 53.37: 61 53.37 - 71.16: 15 71.16 - 88.95: 1 Dihedral angle restraints: 2537 sinusoidal: 957 harmonic: 1580 Sorted by residual: dihedral pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" C TYR A 205 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual -122.60 -131.34 8.74 0 2.50e+00 1.60e-01 1.22e+01 dihedral pdb=" CA ASP A 64 " pdb=" CB ASP A 64 " pdb=" CG ASP A 64 " pdb=" OD1 ASP A 64 " ideal model delta sinusoidal sigma weight residual -30.00 -89.91 59.91 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 2534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 633 0.067 - 0.135: 54 0.135 - 0.202: 3 0.202 - 0.270: 0 0.270 - 0.337: 1 Chirality restraints: 691 Sorted by residual: chirality pdb=" CA TYR A 205 " pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CB TYR A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB VAL A 70 " pdb=" CA VAL A 70 " pdb=" CG1 VAL A 70 " pdb=" CG2 VAL A 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CAL LNR A 702 " pdb=" CAH LNR A 702 " pdb=" CAK LNR A 702 " pdb=" OAD LNR A 702 " both_signs ideal model delta sigma weight residual False -2.28 -2.43 0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 688 not shown) Planarity restraints: 751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C ILE A 103 " -0.060 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 89 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.03e+01 pdb=" C ASN A 89 " 0.056 2.00e-02 2.50e+03 pdb=" O ASN A 89 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY A 90 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 88 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C LYS A 88 " -0.051 2.00e-02 2.50e+03 pdb=" O LYS A 88 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 89 " 0.017 2.00e-02 2.50e+03 ... (remaining 748 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 79 2.69 - 3.25: 4446 3.25 - 3.80: 7147 3.80 - 4.35: 9270 4.35 - 4.90: 16096 Nonbonded interactions: 37038 Sorted by model distance: nonbonded pdb=" OD1 ASP A 75 " pdb=" OG SER A 419 " model vdw 2.142 3.040 nonbonded pdb=" O ALA A 328 " pdb=" OG SER A 331 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASN A 337 " pdb=" N ASN A 338 " model vdw 2.287 3.120 nonbonded pdb=" O THR A 283 " pdb=" OG1 THR A 283 " model vdw 2.327 3.040 nonbonded pdb=" N ASP A 175 " pdb=" OD1 ASP A 175 " model vdw 2.367 3.120 ... (remaining 37033 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: 0.500 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.310 Find NCS groups from input model: 0.040 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:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 4538 Z= 0.236 Angle : 0.544 6.527 6190 Z= 0.292 Chirality : 0.040 0.337 691 Planarity : 0.004 0.039 751 Dihedral : 16.022 88.952 1528 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.08 % Allowed : 19.52 % Favored : 79.39 % 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: 1.96 (0.38), residues: 543 helix: 1.68 (0.28), residues: 376 sheet: None (None), residues: 0 loop : 0.60 (0.53), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.001 0.000 HIS A 296 PHE 0.009 0.001 PHE A 362 TYR 0.018 0.001 TYR A 151 ARG 0.001 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.487 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 57 average time/residue: 0.7522 time to fit residues: 45.8905 Evaluate side-chains 54 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 498 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4538 Z= 0.231 Angle : 0.531 8.089 6190 Z= 0.277 Chirality : 0.040 0.150 691 Planarity : 0.004 0.047 751 Dihedral : 5.938 58.160 607 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.17 % Allowed : 16.49 % Favored : 81.34 % 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: 1.94 (0.38), residues: 543 helix: 1.69 (0.27), residues: 382 sheet: None (None), residues: 0 loop : 0.47 (0.54), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.016 0.001 PHE A 101 TYR 0.017 0.001 TYR A 84 ARG 0.002 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.419 Fit side-chains REVERT: A 329 PHE cc_start: 0.8061 (m-80) cc_final: 0.7716 (m-10) REVERT: A 459 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.6712 (t80) outliers start: 10 outliers final: 2 residues processed: 55 average time/residue: 0.6363 time to fit residues: 37.7771 Evaluate side-chains 48 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 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 436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4538 Z= 0.212 Angle : 0.501 7.306 6190 Z= 0.264 Chirality : 0.040 0.151 691 Planarity : 0.004 0.048 751 Dihedral : 5.195 54.074 602 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.95 % Allowed : 17.14 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.37), residues: 543 helix: 1.65 (0.27), residues: 384 sheet: None (None), residues: 0 loop : 0.57 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.012 0.001 PHE A 110 TYR 0.017 0.001 TYR A 84 ARG 0.002 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8081 (m-80) cc_final: 0.7765 (m-10) REVERT: A 459 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.6580 (t80) REVERT: A 509 MET cc_start: 0.8396 (mtp) cc_final: 0.7851 (mtm) outliers start: 9 outliers final: 4 residues processed: 55 average time/residue: 0.6374 time to fit residues: 37.8814 Evaluate side-chains 49 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4538 Z= 0.216 Angle : 0.502 7.775 6190 Z= 0.265 Chirality : 0.039 0.150 691 Planarity : 0.004 0.051 751 Dihedral : 5.055 48.616 602 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.60 % Allowed : 17.79 % Favored : 79.61 % 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: 1.95 (0.37), residues: 543 helix: 1.67 (0.27), residues: 386 sheet: None (None), residues: 0 loop : 0.52 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.012 0.001 PHE A 110 TYR 0.017 0.001 TYR A 84 ARG 0.001 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8561 (m110) cc_final: 0.8054 (m110) REVERT: A 329 PHE cc_start: 0.8014 (m-80) cc_final: 0.7675 (m-10) REVERT: A 459 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.6624 (t80) REVERT: A 509 MET cc_start: 0.8447 (mtp) cc_final: 0.7916 (mtm) outliers start: 12 outliers final: 4 residues processed: 55 average time/residue: 0.6549 time to fit residues: 38.8428 Evaluate side-chains 49 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 507 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4538 Z= 0.253 Angle : 0.521 8.409 6190 Z= 0.274 Chirality : 0.040 0.154 691 Planarity : 0.004 0.051 751 Dihedral : 5.064 43.494 602 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.39 % Allowed : 17.79 % Favored : 79.83 % 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: 1.88 (0.37), residues: 543 helix: 1.63 (0.27), residues: 385 sheet: None (None), residues: 0 loop : 0.46 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.003 0.000 HIS A 280 PHE 0.011 0.001 PHE A 110 TYR 0.019 0.001 TYR A 84 ARG 0.001 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8074 (m-80) cc_final: 0.7736 (m-10) REVERT: A 365 LEU cc_start: 0.6974 (pp) cc_final: 0.6646 (pt) REVERT: A 371 GLU cc_start: 0.7821 (tp30) cc_final: 0.7308 (tt0) REVERT: A 459 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.6850 (t80) REVERT: A 509 MET cc_start: 0.8387 (mtp) cc_final: 0.7875 (mtm) outliers start: 11 outliers final: 5 residues processed: 52 average time/residue: 0.6945 time to fit residues: 38.8708 Evaluate side-chains 47 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 0.0060 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4538 Z= 0.173 Angle : 0.476 6.631 6190 Z= 0.251 Chirality : 0.038 0.145 691 Planarity : 0.004 0.052 751 Dihedral : 4.665 37.827 602 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.95 % Allowed : 19.09 % Favored : 78.96 % 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: 2.11 (0.37), residues: 543 helix: 1.84 (0.27), residues: 383 sheet: None (None), residues: 0 loop : 0.46 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.001 0.000 HIS A 280 PHE 0.011 0.001 PHE A 110 TYR 0.015 0.001 TYR A 84 ARG 0.001 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8542 (m110) cc_final: 0.8274 (m-40) REVERT: A 329 PHE cc_start: 0.8022 (m-80) cc_final: 0.7695 (m-10) REVERT: A 371 GLU cc_start: 0.7814 (tp30) cc_final: 0.7306 (tt0) REVERT: A 459 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.6685 (t80) REVERT: A 509 MET cc_start: 0.8386 (mtp) cc_final: 0.7913 (mtm) REVERT: A 587 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6843 (mtt90) outliers start: 9 outliers final: 4 residues processed: 55 average time/residue: 0.7881 time to fit residues: 46.3087 Evaluate side-chains 50 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 587 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 52 optimal weight: 0.2980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4538 Z= 0.195 Angle : 0.489 7.341 6190 Z= 0.257 Chirality : 0.039 0.151 691 Planarity : 0.004 0.052 751 Dihedral : 4.446 31.965 600 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.82 % Allowed : 20.17 % Favored : 77.01 % 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: 2.08 (0.37), residues: 543 helix: 1.84 (0.27), residues: 384 sheet: None (None), residues: 0 loop : 0.39 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.011 0.001 PHE A 110 TYR 0.016 0.001 TYR A 84 ARG 0.001 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.523 Fit side-chains REVERT: A 78 ASN cc_start: 0.8544 (m110) cc_final: 0.8268 (m-40) REVERT: A 329 PHE cc_start: 0.8021 (m-80) cc_final: 0.7699 (m-10) REVERT: A 371 GLU cc_start: 0.7773 (tp30) cc_final: 0.7265 (tt0) REVERT: A 459 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.6676 (t80) REVERT: A 509 MET cc_start: 0.8335 (mtp) cc_final: 0.7875 (mtm) outliers start: 13 outliers final: 4 residues processed: 55 average time/residue: 0.7768 time to fit residues: 45.8611 Evaluate side-chains 47 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4538 Z= 0.213 Angle : 0.496 7.628 6190 Z= 0.261 Chirality : 0.039 0.154 691 Planarity : 0.004 0.052 751 Dihedral : 4.505 32.816 600 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.74 % Allowed : 21.04 % Favored : 77.22 % 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: 1.99 (0.37), residues: 543 helix: 1.74 (0.27), residues: 386 sheet: None (None), residues: 0 loop : 0.41 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.010 0.001 PHE A 110 TYR 0.017 0.001 TYR A 84 ARG 0.001 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.479 Fit side-chains REVERT: A 78 ASN cc_start: 0.8535 (m110) cc_final: 0.8059 (m110) REVERT: A 329 PHE cc_start: 0.8019 (m-80) cc_final: 0.7692 (m-10) REVERT: A 371 GLU cc_start: 0.7728 (tp30) cc_final: 0.7214 (tt0) REVERT: A 459 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.6745 (t80) REVERT: A 509 MET cc_start: 0.8309 (mtp) cc_final: 0.7830 (mtm) outliers start: 8 outliers final: 4 residues processed: 51 average time/residue: 0.6856 time to fit residues: 37.7798 Evaluate side-chains 46 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4538 Z= 0.187 Angle : 0.481 6.747 6190 Z= 0.253 Chirality : 0.039 0.150 691 Planarity : 0.004 0.052 751 Dihedral : 4.387 31.621 600 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.08 % Allowed : 21.69 % Favored : 77.22 % 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: 2.08 (0.37), residues: 543 helix: 1.85 (0.27), residues: 384 sheet: None (None), residues: 0 loop : 0.37 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.011 0.001 PHE A 110 TYR 0.015 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.478 Fit side-chains REVERT: A 78 ASN cc_start: 0.8485 (m110) cc_final: 0.8000 (m110) REVERT: A 329 PHE cc_start: 0.8015 (m-80) cc_final: 0.7691 (m-10) REVERT: A 371 GLU cc_start: 0.7722 (tp30) cc_final: 0.7211 (tt0) REVERT: A 459 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.6657 (t80) REVERT: A 509 MET cc_start: 0.8302 (mtp) cc_final: 0.7876 (mtm) outliers start: 5 outliers final: 3 residues processed: 50 average time/residue: 0.7773 time to fit residues: 41.5470 Evaluate side-chains 48 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4538 Z= 0.190 Angle : 0.484 7.167 6190 Z= 0.254 Chirality : 0.039 0.151 691 Planarity : 0.004 0.051 751 Dihedral : 4.410 31.910 600 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.74 % Allowed : 21.04 % Favored : 77.22 % 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: 2.09 (0.37), residues: 543 helix: 1.83 (0.27), residues: 384 sheet: None (None), residues: 0 loop : 0.43 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.010 0.001 PHE A 110 TYR 0.016 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.465 Fit side-chains REVERT: A 78 ASN cc_start: 0.8472 (m110) cc_final: 0.7989 (m110) REVERT: A 329 PHE cc_start: 0.8015 (m-80) cc_final: 0.7694 (m-10) REVERT: A 371 GLU cc_start: 0.7717 (tp30) cc_final: 0.7205 (tt0) REVERT: A 459 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.6677 (t80) REVERT: A 509 MET cc_start: 0.8306 (mtp) cc_final: 0.7873 (mtm) outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.7254 time to fit residues: 39.8097 Evaluate side-chains 50 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 505 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.146033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.111487 restraints weight = 5206.793| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.05 r_work: 0.3181 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4538 Z= 0.204 Angle : 0.493 7.325 6190 Z= 0.259 Chirality : 0.039 0.152 691 Planarity : 0.004 0.051 751 Dihedral : 4.433 32.580 600 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.74 % Allowed : 21.04 % Favored : 77.22 % 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: 2.05 (0.37), residues: 543 helix: 1.80 (0.27), residues: 386 sheet: None (None), residues: 0 loop : 0.42 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 PHE 0.010 0.001 PHE A 110 TYR 0.017 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1548.42 seconds wall clock time: 28 minutes 47.39 seconds (1727.39 seconds total)