Starting phenix.real_space_refine on Fri Nov 15 10:25:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3v_35157/11_2024/8i3v_35157_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3v_35157/11_2024/8i3v_35157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3v_35157/11_2024/8i3v_35157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3v_35157/11_2024/8i3v_35157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3v_35157/11_2024/8i3v_35157_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3v_35157/11_2024/8i3v_35157_trim.cif" } resolution = 2.85 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= 0.003 sd= 0.135 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: 7 Type Number sf(0) Gaussians S 20 5.16 5 Cl 1 4.86 5 C 2965 2.51 5 N 681 2.21 5 O 751 1.98 5 F 1 1.80 5 H 4373 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8792 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8756 Classifications: {'peptide': 548} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 528} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 36 Unusual residues: {' CL': 1, '68P': 1} Classifications: {'undetermined': 2, 'water': 11} Link IDs: {None: 12} Time building chain proxies: 4.50, per 1000 atoms: 0.51 Number of scatterers: 8792 At special positions: 0 Unit cell: (70.3625, 70.3625, 98.5075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 20 16.00 F 1 9.00 O 751 8.00 N 681 7.00 C 2965 6.00 H 4373 1.00 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: 2.22 Conformation dependent library (CDL) restraints added in 725.1 milliseconds 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1008 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 1 sheets defined 81.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 60 through 73 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.569A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.315A 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 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' 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: 3.560A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.958A 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 removed outlier: 3.610A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) 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 262 through 283 removed outlier: 3.986A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 3.862A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.575A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.727A pdb=" N GLU A 304 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 373 Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.734A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) 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: 3.576A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.604A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 496 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: 3.610A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 592 Processing helix chain 'A' and resid 594 through 601 removed outlier: 3.812A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 5.376A 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 616 removed outlier: 3.808A 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 545 295 hydrogen bonds defined for protein. 849 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: 3.10 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4366 1.03 - 1.23: 13 1.23 - 1.42: 2017 1.42 - 1.62: 2497 1.62 - 1.81: 31 Bond restraints: 8924 Sorted by residual: bond pdb=" N GLY A 60 " pdb=" CA GLY A 60 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.20e+00 bond pdb=" N GLY A 60 " pdb=" H GLY A 60 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" CA LEU A 102 " pdb=" C LEU A 102 " ideal model delta sigma weight residual 1.524 1.509 0.016 1.28e-02 6.10e+03 1.48e+00 bond pdb=" C23 68P A 701 " pdb=" N03 68P A 701 " ideal model delta sigma weight residual 1.447 1.467 -0.020 2.00e-02 2.50e+03 9.68e-01 bond pdb=" C05 68P A 701 " pdb=" O02 68P A 701 " ideal model delta sigma weight residual 1.420 1.440 -0.020 2.00e-02 2.50e+03 9.59e-01 ... (remaining 8919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.28: 16077 7.28 - 14.56: 0 14.56 - 21.84: 0 21.84 - 29.12: 0 29.12 - 36.40: 3 Bond angle restraints: 16080 Sorted by residual: angle pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 109.00 72.60 36.40 3.00e+00 1.11e-01 1.47e+02 angle pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 110.00 76.44 33.56 3.00e+00 1.11e-01 1.25e+02 angle pdb=" CB TYR A 205 " pdb=" CA TYR A 205 " pdb=" HA TYR A 205 " ideal model delta sigma weight residual 109.00 77.56 31.44 3.00e+00 1.11e-01 1.10e+02 angle pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" C TYR A 205 " ideal model delta sigma weight residual 110.80 117.86 -7.06 2.13e+00 2.20e-01 1.10e+01 angle pdb=" N LEU A 102 " pdb=" CA LEU A 102 " pdb=" C LEU A 102 " ideal model delta sigma weight residual 111.02 108.23 2.79 1.22e+00 6.72e-01 5.21e+00 ... (remaining 16075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 3735 17.26 - 34.52: 337 34.52 - 51.79: 122 51.79 - 69.05: 42 69.05 - 86.31: 3 Dihedral angle restraints: 4239 sinusoidal: 2156 harmonic: 2083 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 -157.31 -22.69 0 5.00e+00 4.00e-02 2.06e+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 -132.20 9.60 0 2.50e+00 1.60e-01 1.47e+01 dihedral pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual 122.80 131.67 -8.87 0 2.50e+00 1.60e-01 1.26e+01 ... (remaining 4236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 664 0.082 - 0.164: 26 0.164 - 0.245: 0 0.245 - 0.327: 0 0.327 - 0.409: 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 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA ILE A 103 " pdb=" N ILE A 103 " pdb=" C ILE A 103 " pdb=" CB ILE A 103 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA PRO A 132 " pdb=" N PRO A 132 " pdb=" C PRO A 132 " pdb=" CB PRO A 132 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 688 not shown) Planarity restraints: 1279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C ILE A 103 " -0.063 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 492 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C VAL A 492 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL A 492 " 0.016 2.00e-02 2.50e+03 pdb=" N SER A 493 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 102 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C LEU A 102 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU A 102 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE A 103 " 0.011 2.00e-02 2.50e+03 ... (remaining 1276 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 857 2.24 - 2.83: 19092 2.83 - 3.42: 23948 3.42 - 4.01: 32553 4.01 - 4.60: 50443 Nonbonded interactions: 126893 Sorted by model distance: nonbonded pdb="HE21 GLN A 234 " pdb=" OE1 GLN A 236 " model vdw 1.646 2.450 nonbonded pdb=" HA TYR A 205 " pdb=" HB3 TYR A 205 " model vdw 1.665 1.952 nonbonded pdb=" HH TYR A 496 " pdb=" OD2 ASP A 504 " model vdw 1.665 2.450 nonbonded pdb="HH22 ARG A 121 " pdb=" O ASN A 333 " model vdw 1.673 2.450 nonbonded pdb=" HH TYR A 162 " pdb=" O HOH A 803 " model vdw 1.699 2.450 ... (remaining 126888 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: 0.300 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: 0.160 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 21.950 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.003 0.040 4551 Z= 0.189 Angle : 0.538 7.058 6210 Z= 0.285 Chirality : 0.039 0.409 691 Planarity : 0.004 0.037 752 Dihedral : 16.333 86.310 1542 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.61 % Rotamer: Outliers : 2.16 % Allowed : 20.78 % Favored : 77.06 % 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: 1.90 (0.38), residues: 544 helix: 1.66 (0.28), residues: 376 sheet: None (None), residues: 0 loop : 0.54 (0.54), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 235 HIS 0.002 0.001 HIS A 228 PHE 0.017 0.001 PHE A 408 TYR 0.014 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.622 Fit side-chains REVERT: A 100 LEU cc_start: 0.8089 (tp) cc_final: 0.7884 (tp) outliers start: 10 outliers final: 7 residues processed: 51 average time/residue: 1.2482 time to fit residues: 69.0160 Evaluate side-chains 49 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 399 SER 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: 1.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4551 Z= 0.293 Angle : 0.553 7.336 6210 Z= 0.291 Chirality : 0.042 0.418 691 Planarity : 0.004 0.037 752 Dihedral : 5.594 55.586 621 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.61 % Rotamer: Outliers : 2.38 % Allowed : 18.83 % Favored : 78.79 % 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: 1.55 (0.37), residues: 544 helix: 1.43 (0.27), residues: 383 sheet: None (None), residues: 0 loop : 0.24 (0.53), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 128 HIS 0.003 0.001 HIS A 441 PHE 0.016 0.002 PHE A 408 TYR 0.017 0.001 TYR A 84 ARG 0.002 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.713 Fit side-chains REVERT: A 152 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.7702 (t80) REVERT: A 431 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.7911 (mm) REVERT: A 603 GLN cc_start: 0.7916 (mt0) cc_final: 0.7218 (mm110) outliers start: 11 outliers final: 4 residues processed: 57 average time/residue: 1.3711 time to fit residues: 84.1329 Evaluate side-chains 52 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 431 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4551 Z= 0.229 Angle : 0.515 6.986 6210 Z= 0.270 Chirality : 0.040 0.415 691 Planarity : 0.004 0.036 752 Dihedral : 5.400 57.631 616 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 2.16 % Allowed : 18.61 % Favored : 79.22 % 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: 1.72 (0.37), residues: 544 helix: 1.64 (0.27), residues: 379 sheet: None (None), residues: 0 loop : 0.10 (0.52), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 235 HIS 0.003 0.001 HIS A 599 PHE 0.014 0.001 PHE A 408 TYR 0.015 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.676 Fit side-chains REVERT: A 152 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.7707 (t80) REVERT: A 431 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.7865 (mm) REVERT: A 603 GLN cc_start: 0.7925 (mt0) cc_final: 0.7231 (mm110) outliers start: 10 outliers final: 5 residues processed: 51 average time/residue: 1.1614 time to fit residues: 64.8449 Evaluate side-chains 48 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 600 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4551 Z= 0.215 Angle : 0.504 6.970 6210 Z= 0.264 Chirality : 0.040 0.413 691 Planarity : 0.004 0.038 752 Dihedral : 4.613 19.495 614 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 1.73 % Allowed : 19.26 % Favored : 79.00 % 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: 1.80 (0.37), residues: 544 helix: 1.76 (0.27), residues: 374 sheet: None (None), residues: 0 loop : 0.01 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.002 0.001 HIS A 599 PHE 0.011 0.001 PHE A 362 TYR 0.015 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.652 Fit side-chains REVERT: A 152 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.7712 (t80) REVERT: A 431 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.7786 (mm) REVERT: A 603 GLN cc_start: 0.7942 (mt0) cc_final: 0.7240 (mm110) outliers start: 8 outliers final: 3 residues processed: 50 average time/residue: 1.0946 time to fit residues: 59.9815 Evaluate side-chains 45 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 431 LEU 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: 8.9990 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7988 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4551 Z= 0.172 Angle : 0.481 6.779 6210 Z= 0.252 Chirality : 0.039 0.410 691 Planarity : 0.004 0.039 752 Dihedral : 4.362 17.006 613 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 1.95 % Allowed : 18.40 % Favored : 79.65 % 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: 1.87 (0.37), residues: 544 helix: 1.81 (0.27), residues: 376 sheet: None (None), residues: 0 loop : 0.03 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 235 HIS 0.002 0.001 HIS A 599 PHE 0.011 0.001 PHE A 362 TYR 0.013 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.639 Fit side-chains REVERT: A 152 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.7661 (t80) REVERT: A 341 ARG cc_start: 0.7390 (ttm170) cc_final: 0.7147 (tmm160) REVERT: A 603 GLN cc_start: 0.7950 (mt0) cc_final: 0.7240 (mm110) outliers start: 9 outliers final: 2 residues processed: 53 average time/residue: 1.3523 time to fit residues: 77.1696 Evaluate side-chains 48 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 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: 0.9990 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7991 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4551 Z= 0.177 Angle : 0.480 6.753 6210 Z= 0.251 Chirality : 0.039 0.411 691 Planarity : 0.004 0.039 752 Dihedral : 4.354 17.310 613 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 2.16 % Allowed : 18.83 % Favored : 79.00 % 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: 1.90 (0.37), residues: 544 helix: 1.81 (0.27), residues: 377 sheet: None (None), residues: 0 loop : 0.10 (0.52), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 235 HIS 0.002 0.001 HIS A 599 PHE 0.010 0.001 PHE A 362 TYR 0.014 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.696 Fit side-chains REVERT: A 152 TYR cc_start: 0.8836 (OUTLIER) cc_final: 0.7676 (t80) REVERT: A 341 ARG cc_start: 0.7451 (ttm170) cc_final: 0.7213 (tmm160) REVERT: A 431 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7812 (mm) outliers start: 10 outliers final: 3 residues processed: 52 average time/residue: 1.3148 time to fit residues: 74.0811 Evaluate side-chains 48 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 0.0770 chunk 31 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- 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: 0.7973 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4551 Z= 0.150 Angle : 0.467 6.661 6210 Z= 0.243 Chirality : 0.039 0.410 691 Planarity : 0.004 0.037 752 Dihedral : 4.117 14.619 613 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 1.73 % Allowed : 19.26 % Favored : 79.00 % 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: 2.03 (0.37), residues: 544 helix: 1.94 (0.27), residues: 375 sheet: None (None), residues: 0 loop : 0.07 (0.52), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 235 HIS 0.002 0.001 HIS A 599 PHE 0.010 0.001 PHE A 362 TYR 0.012 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.668 Fit side-chains REVERT: A 152 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.7556 (t80) REVERT: A 242 MET cc_start: 0.8273 (mtp) cc_final: 0.8036 (mtm) REVERT: A 341 ARG cc_start: 0.7416 (ttm170) cc_final: 0.7190 (tmm160) REVERT: A 459 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.6917 (t80) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 1.0795 time to fit residues: 61.4214 Evaluate side-chains 48 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 298 ASP 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: 2.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4551 Z= 0.266 Angle : 0.521 6.892 6210 Z= 0.275 Chirality : 0.041 0.419 691 Planarity : 0.004 0.040 752 Dihedral : 4.875 25.486 613 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.65 % Favored : 98.16 % Rotamer: Outliers : 1.73 % Allowed : 19.70 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.37), residues: 544 helix: 1.72 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -0.05 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 128 HIS 0.002 0.001 HIS A 613 PHE 0.015 0.001 PHE A 362 TYR 0.019 0.001 TYR A 84 ARG 0.003 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.595 Fit side-chains REVERT: A 152 TYR cc_start: 0.8906 (OUTLIER) cc_final: 0.7777 (t80) REVERT: A 603 GLN cc_start: 0.7985 (mt0) cc_final: 0.7268 (mm110) outliers start: 8 outliers final: 2 residues processed: 53 average time/residue: 0.9508 time to fit residues: 56.0219 Evaluate side-chains 46 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 256 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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: 0.7996 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4551 Z= 0.176 Angle : 0.481 6.607 6210 Z= 0.251 Chirality : 0.039 0.411 691 Planarity : 0.004 0.037 752 Dihedral : 4.313 16.777 613 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.02 % Favored : 97.79 % Rotamer: Outliers : 1.08 % Allowed : 20.35 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.37), residues: 544 helix: 1.83 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -0.01 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.002 0.001 HIS A 599 PHE 0.010 0.001 PHE A 362 TYR 0.013 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.675 Fit side-chains REVERT: A 152 TYR cc_start: 0.8844 (OUTLIER) cc_final: 0.7625 (t80) REVERT: A 341 ARG cc_start: 0.7387 (ttm170) cc_final: 0.7142 (tmm160) outliers start: 5 outliers final: 2 residues processed: 45 average time/residue: 1.2405 time to fit residues: 60.8128 Evaluate side-chains 42 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 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: 0.7986 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4551 Z= 0.163 Angle : 0.476 6.573 6210 Z= 0.248 Chirality : 0.039 0.411 691 Planarity : 0.004 0.037 752 Dihedral : 4.194 15.397 613 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 0.87 % Allowed : 20.56 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.37), residues: 544 helix: 1.89 (0.27), residues: 376 sheet: None (None), residues: 0 loop : 0.02 (0.52), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.002 0.001 HIS A 599 PHE 0.010 0.001 PHE A 362 TYR 0.013 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) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.712 Fit side-chains REVERT: A 152 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.7579 (t80) REVERT: A 341 ARG cc_start: 0.7393 (ttm170) cc_final: 0.7148 (tmm160) REVERT: A 374 VAL cc_start: 0.8771 (m) cc_final: 0.8549 (p) outliers start: 4 outliers final: 3 residues processed: 46 average time/residue: 1.3740 time to fit residues: 68.3379 Evaluate side-chains 44 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 256 VAL 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 44 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.102538 restraints weight = 15271.686| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.68 r_work: 0.3063 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4551 Z= 0.211 Angle : 0.506 6.677 6210 Z= 0.263 Chirality : 0.040 0.415 691 Planarity : 0.004 0.038 752 Dihedral : 4.484 19.780 613 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.84 % Favored : 97.98 % Rotamer: Outliers : 0.87 % Allowed : 21.21 % Favored : 77.92 % 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: 1.86 (0.37), residues: 544 helix: 1.82 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.01 (0.51), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 235 HIS 0.002 0.001 HIS A 599 PHE 0.012 0.001 PHE A 362 TYR 0.016 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2955.24 seconds wall clock time: 53 minutes 1.95 seconds (3181.95 seconds total)