Starting phenix.real_space_refine on Mon Feb 10 22:51:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bg6_16024/02_2025/8bg6_16024.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bg6_16024/02_2025/8bg6_16024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bg6_16024/02_2025/8bg6_16024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bg6_16024/02_2025/8bg6_16024.map" model { file = "/net/cci-nas-00/data/ceres_data/8bg6_16024/02_2025/8bg6_16024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bg6_16024/02_2025/8bg6_16024.cif" } resolution = 4.11 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 ------------------------------------------------------------------------------- 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= 0.017 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 16 5.16 5 C 1981 2.51 5 N 527 2.21 5 O 600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3124 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 845 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1450 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 172} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" 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: 2.84, per 1000 atoms: 0.91 Number of scatterers: 3124 At special positions: 0 Unit cell: (66.64, 65.96, 94.52, 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 16 16.00 O 600 8.00 N 527 7.00 C 1981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=1.94 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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 E2000 " - " ASN E 343 " Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 424.5 milliseconds 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 728 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 8.3% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.596A pdb=" N THR A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 342 removed outlier: 3.781A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.681A pdb=" N ALA E 352 " --> pdb=" O SER E 349 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 349 through 353' Processing helix chain 'E' and resid 384 through 388 removed outlier: 3.579A pdb=" N LEU E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 384 through 388' Processing helix chain 'E' and resid 404 through 410 removed outlier: 3.683A pdb=" N VAL E 407 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.583A pdb=" N SER A 21 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.072A pdb=" N GLY A 10 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 37 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.524A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR B 49 " --> pdb=" O HIS B 53 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS B 53 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 19 through 24 Processing sheet with id=AA5, first strand: chain 'E' and resid 355 through 358 removed outlier: 7.161A pdb=" N ASN E 437 " --> pdb=" O PHE E 374 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE E 374 " --> pdb=" O ASN E 437 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 453 Processing sheet with id=AA7, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.500A pdb=" N TYR E 473 " --> pdb=" O TYR E 489 " (cutoff:3.500A) 85 hydrogen bonds defined for protein. 198 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.81 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 757 1.33 - 1.45: 729 1.45 - 1.57: 1696 1.57 - 1.69: 0 1.69 - 1.82: 20 Bond restraints: 3202 Sorted by residual: bond pdb=" N SER A 31 " pdb=" CA SER A 31 " ideal model delta sigma weight residual 1.458 1.485 -0.026 9.00e-03 1.23e+04 8.67e+00 bond pdb=" N ASN E 343 " pdb=" CA ASN E 343 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.06e-02 8.90e+03 8.49e+00 bond pdb=" N GLU A 26 " pdb=" CA GLU A 26 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.23e-02 6.61e+03 8.41e+00 bond pdb=" N VAL E 362 " pdb=" CA VAL E 362 " ideal model delta sigma weight residual 1.459 1.492 -0.034 1.19e-02 7.06e+03 8.09e+00 bond pdb=" N TYR A 93 " pdb=" CA TYR A 93 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.16e-02 7.43e+03 7.95e+00 ... (remaining 3197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 4044 1.73 - 3.46: 254 3.46 - 5.19: 44 5.19 - 6.93: 7 6.93 - 8.66: 3 Bond angle restraints: 4352 Sorted by residual: angle pdb=" CB LYS E 386 " pdb=" CG LYS E 386 " pdb=" CD LYS E 386 " ideal model delta sigma weight residual 111.30 119.96 -8.66 2.30e+00 1.89e-01 1.42e+01 angle pdb=" CA THR A 108 " pdb=" C THR A 108 " pdb=" O THR A 108 " ideal model delta sigma weight residual 121.46 117.15 4.31 1.17e+00 7.31e-01 1.36e+01 angle pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" O ILE A 103 " ideal model delta sigma weight residual 120.25 116.69 3.56 9.90e-01 1.02e+00 1.29e+01 angle pdb=" C ILE A 103 " pdb=" N TRP A 104 " pdb=" CA TRP A 104 " ideal model delta sigma weight residual 123.00 127.93 -4.93 1.38e+00 5.25e-01 1.28e+01 angle pdb=" CA GLN E 474 " pdb=" CB GLN E 474 " pdb=" CG GLN E 474 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.21e+01 ... (remaining 4347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 1706 15.98 - 31.95: 144 31.95 - 47.93: 39 47.93 - 63.91: 5 63.91 - 79.88: 2 Dihedral angle restraints: 1896 sinusoidal: 746 harmonic: 1150 Sorted by residual: dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 161.54 -68.54 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CA GLY A 105 " pdb=" C GLY A 105 " pdb=" N GLN A 106 " pdb=" CA GLN A 106 " ideal model delta harmonic sigma weight residual -180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" C SER A 31 " pdb=" N SER A 31 " pdb=" CA SER A 31 " pdb=" CB SER A 31 " ideal model delta harmonic sigma weight residual -122.60 -131.69 9.09 0 2.50e+00 1.60e-01 1.32e+01 ... (remaining 1893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 377 0.068 - 0.136: 75 0.136 - 0.204: 15 0.204 - 0.272: 0 0.272 - 0.340: 2 Chirality restraints: 469 Sorted by residual: 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 2.77 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA SER A 31 " pdb=" N SER A 31 " pdb=" C SER A 31 " pdb=" CB SER A 31 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA ASN A 76 " pdb=" N ASN A 76 " pdb=" C ASN A 76 " pdb=" CB ASN A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 466 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 40 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PRO A 41 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 96 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C ALA A 96 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA A 96 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG A 97 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 16 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C GLY A 16 " 0.033 2.00e-02 2.50e+03 pdb=" O GLY A 16 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 17 " -0.011 2.00e-02 2.50e+03 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1161 2.86 - 3.37: 2456 3.37 - 3.88: 4514 3.88 - 4.39: 4882 4.39 - 4.90: 8948 Nonbonded interactions: 21961 Sorted by model distance: nonbonded pdb=" O ASP B 28 " pdb=" OD1 ASP B 28 " model vdw 2.348 3.040 nonbonded pdb=" O MET A 99 " pdb=" CG ARG A 100 " model vdw 2.425 3.440 nonbonded pdb=" OE1 GLU A 102 " pdb=" OH TYR B 36 " model vdw 2.463 3.040 nonbonded pdb=" OD1 ASN E 448 " pdb=" N ASN E 450 " model vdw 2.473 3.120 nonbonded pdb=" O SER E 366 " pdb=" N TYR E 369 " model vdw 2.496 3.120 ... (remaining 21956 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.410 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 3202 Z= 0.400 Angle : 0.937 8.657 4352 Z= 0.604 Chirality : 0.060 0.340 469 Planarity : 0.005 0.068 565 Dihedral : 12.582 79.885 1156 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.90 (0.43), residues: 392 helix: -3.56 (0.97), residues: 18 sheet: 0.73 (0.50), residues: 116 loop : -1.06 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 436 HIS 0.006 0.002 HIS B 90 PHE 0.011 0.001 PHE E 400 TYR 0.014 0.001 TYR E 473 ARG 0.002 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1593 time to fit residues: 15.4440 Evaluate side-chains 61 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.0470 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS B 34 ASN ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.144168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.120475 restraints weight = 4366.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.118813 restraints weight = 5744.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.116688 restraints weight = 5928.176| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3202 Z= 0.169 Angle : 0.565 5.110 4352 Z= 0.301 Chirality : 0.045 0.136 469 Planarity : 0.004 0.035 565 Dihedral : 4.069 14.609 461 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.35 (0.44), residues: 392 helix: -3.43 (0.95), residues: 18 sheet: 0.62 (0.50), residues: 127 loop : -0.41 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 436 HIS 0.003 0.001 HIS B 90 PHE 0.010 0.001 PHE E 490 TYR 0.014 0.001 TYR E 453 ARG 0.004 0.000 ARG E 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8284 (t0) cc_final: 0.8078 (t0) REVERT: A 88 GLU cc_start: 0.7385 (tp30) cc_final: 0.7058 (tp30) REVERT: E 370 ASN cc_start: 0.7890 (p0) cc_final: 0.7668 (p0) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1688 time to fit residues: 16.6235 Evaluate side-chains 64 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.144528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.131415 restraints weight = 4300.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.121702 restraints weight = 6633.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.119147 restraints weight = 6860.248| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3202 Z= 0.211 Angle : 0.556 4.912 4352 Z= 0.299 Chirality : 0.044 0.132 469 Planarity : 0.004 0.037 565 Dihedral : 4.070 14.162 461 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.33 (0.44), residues: 392 helix: -3.02 (0.85), residues: 24 sheet: 0.63 (0.50), residues: 128 loop : -0.35 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 436 HIS 0.002 0.001 HIS B 90 PHE 0.012 0.001 PHE B 73 TYR 0.012 0.002 TYR B 49 ARG 0.002 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.349 Fit side-chains REVERT: A 72 ASP cc_start: 0.8278 (t0) cc_final: 0.7980 (t0) REVERT: A 88 GLU cc_start: 0.7305 (tp30) cc_final: 0.7061 (tp30) REVERT: E 370 ASN cc_start: 0.8241 (p0) cc_final: 0.8004 (p0) REVERT: E 400 PHE cc_start: 0.7610 (m-80) cc_final: 0.7393 (m-80) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1550 time to fit residues: 14.8470 Evaluate side-chains 67 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.148027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.137334 restraints weight = 4342.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.130551 restraints weight = 7455.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.124870 restraints weight = 6115.782| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3202 Z= 0.143 Angle : 0.522 5.698 4352 Z= 0.277 Chirality : 0.044 0.166 469 Planarity : 0.004 0.041 565 Dihedral : 3.925 13.360 461 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.44), residues: 392 helix: -3.14 (0.93), residues: 24 sheet: 0.73 (0.50), residues: 126 loop : -0.12 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 36 HIS 0.003 0.001 HIS B 90 PHE 0.010 0.001 PHE B 73 TYR 0.008 0.001 TYR E 423 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8377 (t0) cc_final: 0.8095 (t0) REVERT: B 79 GLN cc_start: 0.8722 (mp10) cc_final: 0.8478 (mp10) REVERT: E 370 ASN cc_start: 0.8066 (p0) cc_final: 0.7796 (p0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1504 time to fit residues: 14.9242 Evaluate side-chains 69 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 32 optimal weight: 0.0060 chunk 38 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.142230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.130611 restraints weight = 4423.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.122443 restraints weight = 8186.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.117162 restraints weight = 6382.840| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3202 Z= 0.217 Angle : 0.577 5.122 4352 Z= 0.306 Chirality : 0.045 0.132 469 Planarity : 0.004 0.041 565 Dihedral : 4.068 14.217 461 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.14 (0.43), residues: 392 helix: -3.14 (0.92), residues: 24 sheet: 0.74 (0.49), residues: 129 loop : -0.17 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 36 HIS 0.004 0.002 HIS B 53 PHE 0.011 0.001 PHE B 73 TYR 0.012 0.002 TYR B 36 ARG 0.004 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: B 79 GLN cc_start: 0.8778 (mp10) cc_final: 0.8527 (mp10) REVERT: E 370 ASN cc_start: 0.8301 (p0) cc_final: 0.8029 (p0) REVERT: E 400 PHE cc_start: 0.7751 (m-80) cc_final: 0.7440 (m-80) REVERT: E 474 GLN cc_start: 0.7633 (pp30) cc_final: 0.7418 (pp30) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1541 time to fit residues: 14.0736 Evaluate side-chains 68 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.136506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.124234 restraints weight = 4416.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.123649 restraints weight = 8308.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.123496 restraints weight = 7007.884| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3202 Z= 0.221 Angle : 0.581 5.245 4352 Z= 0.309 Chirality : 0.045 0.143 469 Planarity : 0.004 0.044 565 Dihedral : 4.059 13.411 461 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.44), residues: 392 helix: -3.23 (0.89), residues: 24 sheet: 0.64 (0.47), residues: 136 loop : -0.09 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 36 HIS 0.003 0.001 HIS B 90 PHE 0.011 0.001 PHE B 73 TYR 0.012 0.001 TYR B 36 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8219 (t0) cc_final: 0.8015 (t0) REVERT: A 106 GLN cc_start: 0.8086 (tp-100) cc_final: 0.7882 (mm-40) REVERT: B 79 GLN cc_start: 0.8867 (mp10) cc_final: 0.8087 (mp10) REVERT: E 370 ASN cc_start: 0.6911 (p0) cc_final: 0.6701 (p0) REVERT: E 400 PHE cc_start: 0.7747 (m-80) cc_final: 0.7440 (m-80) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1744 time to fit residues: 16.4670 Evaluate side-chains 68 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.136522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.124022 restraints weight = 4444.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.122671 restraints weight = 8776.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.120831 restraints weight = 8234.888| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3202 Z= 0.223 Angle : 0.577 5.122 4352 Z= 0.305 Chirality : 0.045 0.145 469 Planarity : 0.004 0.044 565 Dihedral : 4.065 14.316 461 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.44), residues: 392 helix: -3.21 (0.90), residues: 24 sheet: 0.64 (0.45), residues: 143 loop : -0.10 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 36 HIS 0.003 0.001 HIS B 90 PHE 0.012 0.001 PHE B 73 TYR 0.010 0.001 TYR E 453 ARG 0.004 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8316 (t0) cc_final: 0.8057 (t0) REVERT: A 106 GLN cc_start: 0.8108 (tp-100) cc_final: 0.7880 (mm-40) REVERT: E 370 ASN cc_start: 0.7057 (p0) cc_final: 0.6830 (p0) REVERT: E 400 PHE cc_start: 0.7797 (m-80) cc_final: 0.7460 (m-80) REVERT: E 506 GLN cc_start: 0.8929 (mp-120) cc_final: 0.8590 (mp-120) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1742 time to fit residues: 16.2007 Evaluate side-chains 62 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 0.0870 chunk 26 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 0.1980 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.138713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.110422 restraints weight = 4359.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.109887 restraints weight = 4507.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.109684 restraints weight = 4671.810| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3202 Z= 0.184 Angle : 0.581 5.042 4352 Z= 0.305 Chirality : 0.045 0.130 469 Planarity : 0.004 0.046 565 Dihedral : 3.996 13.567 461 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.09 (0.44), residues: 392 helix: -3.30 (0.86), residues: 24 sheet: 0.48 (0.44), residues: 154 loop : 0.05 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 36 HIS 0.003 0.001 HIS B 90 PHE 0.011 0.001 PHE B 73 TYR 0.009 0.001 TYR E 453 ARG 0.003 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8389 (t0) cc_final: 0.8043 (t0) REVERT: A 81 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7396 (mm-40) REVERT: B 91 CYS cc_start: 0.8896 (t) cc_final: 0.8392 (p) REVERT: E 370 ASN cc_start: 0.8192 (p0) cc_final: 0.7981 (p0) REVERT: E 474 GLN cc_start: 0.7745 (pp30) cc_final: 0.7445 (pp30) REVERT: E 506 GLN cc_start: 0.8925 (mp-120) cc_final: 0.8543 (mp10) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1890 time to fit residues: 16.0933 Evaluate side-chains 65 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 0.0570 chunk 25 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.139026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.128390 restraints weight = 4437.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.123656 restraints weight = 7163.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.117900 restraints weight = 7066.221| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3202 Z= 0.185 Angle : 0.586 5.207 4352 Z= 0.308 Chirality : 0.045 0.132 469 Planarity : 0.004 0.047 565 Dihedral : 3.982 14.653 461 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.03 (0.44), residues: 392 helix: -3.29 (0.86), residues: 24 sheet: 0.56 (0.45), residues: 153 loop : 0.05 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 36 HIS 0.003 0.001 HIS B 90 PHE 0.011 0.001 PHE B 73 TYR 0.009 0.001 TYR E 453 ARG 0.003 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7292 (mm-40) REVERT: B 91 CYS cc_start: 0.8909 (t) cc_final: 0.8464 (p) REVERT: E 370 ASN cc_start: 0.7452 (p0) cc_final: 0.7194 (p0) REVERT: E 474 GLN cc_start: 0.7720 (pp30) cc_final: 0.7487 (pp30) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1835 time to fit residues: 16.0335 Evaluate side-chains 64 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.137894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.125792 restraints weight = 4346.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.117650 restraints weight = 8157.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.113629 restraints weight = 6863.583| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3202 Z= 0.186 Angle : 0.582 5.359 4352 Z= 0.307 Chirality : 0.044 0.131 469 Planarity : 0.004 0.048 565 Dihedral : 3.906 13.668 461 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.00 (0.44), residues: 392 helix: -3.28 (0.87), residues: 24 sheet: 0.61 (0.45), residues: 154 loop : 0.05 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 36 HIS 0.003 0.001 HIS B 90 PHE 0.011 0.001 PHE B 73 TYR 0.008 0.001 TYR E 453 ARG 0.004 0.000 ARG E 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8262 (t0) cc_final: 0.7999 (t0) REVERT: B 91 CYS cc_start: 0.8865 (t) cc_final: 0.8422 (p) REVERT: E 370 ASN cc_start: 0.7951 (p0) cc_final: 0.7718 (p0) REVERT: E 465 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7436 (tp30) REVERT: E 474 GLN cc_start: 0.7764 (pp30) cc_final: 0.7559 (pp30) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1836 time to fit residues: 15.8737 Evaluate side-chains 64 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 0.0980 chunk 3 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.135634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.121831 restraints weight = 4409.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.121417 restraints weight = 8164.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.119715 restraints weight = 7200.605| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3202 Z= 0.251 Angle : 0.606 5.249 4352 Z= 0.321 Chirality : 0.046 0.137 469 Planarity : 0.004 0.047 565 Dihedral : 4.071 14.433 461 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.08 (0.44), residues: 392 helix: -3.28 (0.87), residues: 24 sheet: 0.58 (0.44), residues: 150 loop : -0.03 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 36 HIS 0.002 0.001 HIS B 90 PHE 0.012 0.001 PHE B 73 TYR 0.011 0.002 TYR B 36 ARG 0.004 0.000 ARG E 357 =============================================================================== Job complete usr+sys time: 1519.81 seconds wall clock time: 27 minutes 48.07 seconds (1668.07 seconds total)