Starting phenix.real_space_refine on Mon Jan 13 22:32:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xb4_38210/01_2025/8xb4_38210.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xb4_38210/01_2025/8xb4_38210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xb4_38210/01_2025/8xb4_38210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xb4_38210/01_2025/8xb4_38210.map" model { file = "/net/cci-nas-00/data/ceres_data/8xb4_38210/01_2025/8xb4_38210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xb4_38210/01_2025/8xb4_38210.cif" } resolution = 2.92 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= -0.001 sd= 0.126 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 2894 2.51 5 N 665 2.21 5 O 728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4307 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4293 Classifications: {'peptide': 536} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 516} Chain breaks: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.42, per 1000 atoms: 0.79 Number of scatterers: 4307 At special positions: 0 Unit cell: (65.88, 66.96, 95.04, 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 728 8.00 N 665 7.00 C 2894 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 184 " Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 514.6 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 988 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 81.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 66 through 74 removed outlier: 4.005A pdb=" N PHE A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.525A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.215A 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 105 removed outlier: 3.652A pdb=" N LEU A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 105 through 121 removed outlier: 3.524A pdb=" N LEU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.870A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.713A 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: 3.805A pdb=" N GLY A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 207 removed outlier: 3.505A pdb=" N PHE A 207 " --> pdb=" O LYS A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 207' Processing helix chain 'A' and resid 208 through 218 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 264 through 283 Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.865A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.788A pdb=" N LEU A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 320 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 372 Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.542A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 441 through 456 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.731A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 494 Processing helix chain 'A' and resid 497 through 509 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: 4.293A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 578 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 597 Processing helix chain 'A' and resid 598 through 603 removed outlier: 4.038A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN A 603 " --> pdb=" O HIS A 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 598 through 603' Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.316A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 819 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: 1.13 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1257 1.34 - 1.46: 1195 1.46 - 1.58: 1964 1.58 - 1.70: 0 1.70 - 1.81: 31 Bond restraints: 4447 Sorted by residual: bond pdb=" C3 NAG A 701 " pdb=" O3 NAG A 701 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.86e-01 bond pdb=" C5 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.413 1.432 -0.019 2.00e-02 2.50e+03 9.34e-01 bond pdb=" CG LEU A 390 " pdb=" CD2 LEU A 390 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.20e-01 bond pdb=" C PHE A 82 " pdb=" O PHE A 82 " ideal model delta sigma weight residual 1.244 1.235 0.008 9.80e-03 1.04e+04 6.95e-01 bond pdb=" CB VAL A 535 " pdb=" CG1 VAL A 535 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.43e-01 ... (remaining 4442 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 5756 1.18 - 2.36: 249 2.36 - 3.54: 45 3.54 - 4.72: 11 4.72 - 5.90: 8 Bond angle restraints: 6069 Sorted by residual: angle pdb=" N GLY A 478 " pdb=" CA GLY A 478 " pdb=" C GLY A 478 " ideal model delta sigma weight residual 113.18 107.55 5.63 2.37e+00 1.78e-01 5.64e+00 angle pdb=" C ASN A 596 " pdb=" N GLU A 597 " pdb=" CA GLU A 597 " ideal model delta sigma weight residual 123.17 120.08 3.09 1.49e+00 4.50e-01 4.30e+00 angle pdb=" CA TYR A 391 " pdb=" C TYR A 391 " pdb=" N PRO A 392 " ideal model delta sigma weight residual 118.44 121.69 -3.25 1.59e+00 3.96e-01 4.17e+00 angle pdb=" C VAL A 282 " pdb=" N THR A 283 " pdb=" CA THR A 283 " ideal model delta sigma weight residual 121.94 118.02 3.92 2.00e+00 2.50e-01 3.85e+00 angle pdb=" CA TYR A 111 " pdb=" CB TYR A 111 " pdb=" CG TYR A 111 " ideal model delta sigma weight residual 113.90 117.28 -3.38 1.80e+00 3.09e-01 3.53e+00 ... (remaining 6064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 2352 21.48 - 42.95: 121 42.95 - 64.43: 8 64.43 - 85.90: 7 85.90 - 107.38: 7 Dihedral angle restraints: 2495 sinusoidal: 944 harmonic: 1551 Sorted by residual: dihedral pdb=" CA THR A 544 " pdb=" C THR A 544 " pdb=" N TYR A 545 " pdb=" CA TYR A 545 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" C2 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" C4 NAG A 701 " pdb=" C5 NAG A 701 " ideal model delta sinusoidal sigma weight residual 53.78 -53.60 107.38 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C2 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" C4 NAG A 701 " pdb=" O4 NAG A 701 " ideal model delta sinusoidal sigma weight residual 175.11 68.05 107.06 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 2492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 360 0.029 - 0.058: 208 0.058 - 0.087: 78 0.087 - 0.116: 27 0.116 - 0.145: 8 Chirality restraints: 681 Sorted by residual: chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.25e-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 2.58 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE A 549 " pdb=" N ILE A 549 " pdb=" C ILE A 549 " pdb=" CB ILE A 549 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 678 not shown) Planarity restraints: 737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 82 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO A 83 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 111 " -0.014 2.00e-02 2.50e+03 1.23e-02 3.01e+00 pdb=" CG TYR A 111 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 111 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 111 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 111 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 111 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 111 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 111 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 391 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO A 392 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 392 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 392 " -0.024 5.00e-02 4.00e+02 ... (remaining 734 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1130 2.79 - 3.32: 4134 3.32 - 3.84: 7479 3.84 - 4.37: 9160 4.37 - 4.90: 15607 Nonbonded interactions: 37510 Sorted by model distance: nonbonded pdb=" OH TYR A 496 " pdb=" OD2 ASP A 504 " model vdw 2.258 3.040 nonbonded pdb=" OE2 GLU A 425 " pdb=" OG1 THR A 429 " model vdw 2.279 3.040 nonbonded pdb=" NH1 ARG A 121 " pdb=" O ASN A 333 " model vdw 2.293 3.120 nonbonded pdb=" OD1 ASP A 75 " pdb=" OD1 ASN A 78 " model vdw 2.335 3.040 nonbonded pdb=" O ALA A 589 " pdb=" OG1 THR A 593 " model vdw 2.369 3.040 ... (remaining 37505 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.700 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.005 0.038 4447 Z= 0.292 Angle : 0.606 5.903 6069 Z= 0.329 Chirality : 0.043 0.145 681 Planarity : 0.005 0.045 736 Dihedral : 14.468 107.378 1504 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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 (0.32), residues: 530 helix: -1.09 (0.23), residues: 379 sheet: None (None), residues: 0 loop : -1.19 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 253 HIS 0.005 0.001 HIS A 280 PHE 0.012 0.001 PHE A 316 TYR 0.030 0.002 TYR A 111 ARG 0.003 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.481 Fit side-chains REVERT: A 88 LYS cc_start: 0.8339 (tttp) cc_final: 0.8021 (ttmt) REVERT: A 206 LYS cc_start: 0.7992 (pttm) cc_final: 0.7682 (ptpt) REVERT: A 531 PHE cc_start: 0.7634 (t80) cc_final: 0.7178 (t80) outliers start: 0 outliers final: 1 residues processed: 75 average time/residue: 0.7247 time to fit residues: 57.8766 Evaluate side-chains 54 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 610 GLN A 613 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.134281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.113748 restraints weight = 4941.611| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.49 r_work: 0.3234 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4447 Z= 0.205 Angle : 0.559 6.841 6069 Z= 0.285 Chirality : 0.042 0.173 681 Planarity : 0.005 0.044 736 Dihedral : 5.985 31.440 600 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.55 % Allowed : 9.07 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.35), residues: 530 helix: 0.09 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -0.39 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.003 0.001 HIS A 222 PHE 0.012 0.001 PHE A 409 TYR 0.019 0.002 TYR A 111 ARG 0.001 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.509 Fit side-chains REVERT: A 206 LYS cc_start: 0.8192 (pttm) cc_final: 0.7676 (ptpt) outliers start: 7 outliers final: 1 residues processed: 68 average time/residue: 0.8004 time to fit residues: 57.8498 Evaluate side-chains 56 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 17 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 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.133273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.113298 restraints weight = 4955.797| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.42 r_work: 0.3130 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4447 Z= 0.255 Angle : 0.554 6.094 6069 Z= 0.285 Chirality : 0.042 0.152 681 Planarity : 0.005 0.046 736 Dihedral : 4.778 32.084 600 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.99 % Allowed : 11.50 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.36), residues: 530 helix: 0.49 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.31 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 PHE 0.012 0.001 PHE A 316 TYR 0.020 0.002 TYR A 111 ARG 0.001 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.475 Fit side-chains REVERT: A 206 LYS cc_start: 0.8254 (pttm) cc_final: 0.7715 (ptpt) outliers start: 9 outliers final: 1 residues processed: 65 average time/residue: 0.7319 time to fit residues: 50.6689 Evaluate side-chains 55 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 30 optimal weight: 0.0970 chunk 51 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.133042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.112434 restraints weight = 4999.191| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.49 r_work: 0.3192 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4447 Z= 0.217 Angle : 0.529 6.159 6069 Z= 0.272 Chirality : 0.041 0.141 681 Planarity : 0.005 0.046 736 Dihedral : 4.382 23.015 598 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.21 % Allowed : 12.17 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.36), residues: 530 helix: 0.75 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.15 (0.53), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.003 0.001 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 604 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.450 Fit side-chains REVERT: A 206 LYS cc_start: 0.8298 (pttm) cc_final: 0.7742 (ptpt) REVERT: A 597 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7324 (pm20) outliers start: 10 outliers final: 5 residues processed: 62 average time/residue: 0.6657 time to fit residues: 44.1271 Evaluate side-chains 59 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 235 TRP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 597 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.131536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.110882 restraints weight = 5043.736| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.50 r_work: 0.3098 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4447 Z= 0.263 Angle : 0.551 6.186 6069 Z= 0.284 Chirality : 0.042 0.144 681 Planarity : 0.005 0.047 736 Dihedral : 4.475 23.452 598 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.65 % Allowed : 13.50 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.36), residues: 530 helix: 0.76 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.07 (0.53), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.004 0.001 HIS A 280 PHE 0.014 0.001 PHE A 408 TYR 0.018 0.002 TYR A 84 ARG 0.002 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.543 Fit side-chains REVERT: A 206 LYS cc_start: 0.8386 (pttm) cc_final: 0.7795 (ptpt) outliers start: 12 outliers final: 6 residues processed: 62 average time/residue: 0.7297 time to fit residues: 48.2139 Evaluate side-chains 61 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 235 TRP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 418 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.132846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.112366 restraints weight = 4955.060| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.47 r_work: 0.3107 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4447 Z= 0.218 Angle : 0.532 6.213 6069 Z= 0.273 Chirality : 0.041 0.146 681 Planarity : 0.004 0.047 736 Dihedral : 4.352 21.268 598 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.65 % Allowed : 13.50 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.36), residues: 530 helix: 0.93 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.03 (0.54), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 PHE 0.011 0.001 PHE A 409 TYR 0.016 0.001 TYR A 84 ARG 0.001 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.436 Fit side-chains REVERT: A 206 LYS cc_start: 0.8330 (pttm) cc_final: 0.7747 (ptpt) REVERT: A 373 LYS cc_start: 0.7848 (mmmt) cc_final: 0.7611 (mmmt) outliers start: 12 outliers final: 6 residues processed: 63 average time/residue: 0.7292 time to fit residues: 48.9622 Evaluate side-chains 64 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 235 TRP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 418 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.131961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.111470 restraints weight = 4977.679| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.47 r_work: 0.3101 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4447 Z= 0.244 Angle : 0.545 6.207 6069 Z= 0.280 Chirality : 0.042 0.147 681 Planarity : 0.004 0.047 736 Dihedral : 4.401 21.540 598 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.21 % Allowed : 14.82 % Favored : 82.96 % 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: 0.89 (0.36), residues: 530 helix: 0.90 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.01 (0.54), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 PHE 0.016 0.001 PHE A 408 TYR 0.017 0.001 TYR A 84 ARG 0.001 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.485 Fit side-chains REVERT: A 206 LYS cc_start: 0.8350 (pttm) cc_final: 0.7771 (ptpt) outliers start: 10 outliers final: 6 residues processed: 62 average time/residue: 0.7808 time to fit residues: 51.5328 Evaluate side-chains 64 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 235 TRP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 418 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.132182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.111741 restraints weight = 4938.481| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.46 r_work: 0.3107 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4447 Z= 0.226 Angle : 0.534 6.230 6069 Z= 0.275 Chirality : 0.041 0.149 681 Planarity : 0.004 0.047 736 Dihedral : 4.351 20.696 598 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.99 % Allowed : 15.49 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.36), residues: 530 helix: 0.97 (0.26), residues: 386 sheet: None (None), residues: 0 loop : 0.01 (0.54), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 PHE 0.012 0.001 PHE A 316 TYR 0.016 0.001 TYR A 84 ARG 0.001 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.450 Fit side-chains REVERT: A 373 LYS cc_start: 0.7759 (mmmt) cc_final: 0.7482 (mmmt) REVERT: A 596 ASN cc_start: 0.6968 (p0) cc_final: 0.6689 (p0) outliers start: 9 outliers final: 6 residues processed: 62 average time/residue: 0.6857 time to fit residues: 45.4497 Evaluate side-chains 60 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 235 TRP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 418 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 31 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 43 optimal weight: 0.0000 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.134831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.115092 restraints weight = 5027.475| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.40 r_work: 0.3149 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4447 Z= 0.182 Angle : 0.522 6.076 6069 Z= 0.269 Chirality : 0.040 0.152 681 Planarity : 0.004 0.047 736 Dihedral : 4.213 18.444 598 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.55 % Allowed : 16.37 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.37), residues: 530 helix: 1.05 (0.26), residues: 389 sheet: None (None), residues: 0 loop : 0.08 (0.56), residues: 141 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 0.011 0.001 PHE A 110 TYR 0.015 0.001 TYR A 84 ARG 0.001 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.500 Fit side-chains REVERT: A 580 THR cc_start: 0.8070 (m) cc_final: 0.7434 (p) REVERT: A 596 ASN cc_start: 0.6808 (p0) cc_final: 0.6600 (p0) outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 0.6543 time to fit residues: 43.7300 Evaluate side-chains 64 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 235 TRP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 418 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.133532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.113721 restraints weight = 4959.095| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.41 r_work: 0.3129 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4447 Z= 0.216 Angle : 0.540 6.090 6069 Z= 0.278 Chirality : 0.041 0.156 681 Planarity : 0.004 0.047 736 Dihedral : 4.192 16.421 598 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.55 % Allowed : 17.04 % Favored : 81.42 % 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: 1.08 (0.37), residues: 530 helix: 1.05 (0.26), residues: 388 sheet: None (None), residues: 0 loop : 0.05 (0.55), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.002 0.001 HIS A 280 PHE 0.012 0.001 PHE A 316 TYR 0.016 0.001 TYR A 84 ARG 0.001 0.000 ARG A 604 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.503 Fit side-chains REVERT: A 580 THR cc_start: 0.8058 (m) cc_final: 0.7429 (p) REVERT: A 596 ASN cc_start: 0.6828 (p0) cc_final: 0.6531 (p0) outliers start: 7 outliers final: 6 residues processed: 61 average time/residue: 0.6988 time to fit residues: 45.6259 Evaluate side-chains 62 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 235 TRP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 418 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 4 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 chunk 29 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 43 optimal weight: 0.0670 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.135506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.115809 restraints weight = 4938.838| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.42 r_work: 0.3152 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4447 Z= 0.169 Angle : 0.519 6.039 6069 Z= 0.266 Chirality : 0.040 0.161 681 Planarity : 0.004 0.047 736 Dihedral : 4.044 15.277 598 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.33 % Allowed : 17.26 % Favored : 81.42 % 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: 1.29 (0.37), residues: 530 helix: 1.19 (0.27), residues: 388 sheet: None (None), residues: 0 loop : 0.15 (0.56), residues: 142 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 0.014 0.001 TYR A 84 ARG 0.001 0.000 ARG A 604 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2763.33 seconds wall clock time: 49 minutes 37.43 seconds (2977.43 seconds total)