Starting phenix.real_space_refine on Fri Aug 2 17:10:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/08_2024/7mkm_23899.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/08_2024/7mkm_23899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/08_2024/7mkm_23899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/08_2024/7mkm_23899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/08_2024/7mkm_23899.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/08_2024/7mkm_23899.cif" } resolution = 3.16 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 751 atoms to isotropic. 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 17 5.16 5 C 2030 2.51 5 N 528 2.21 5 O 617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3192 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1500 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 178} Chain: "H" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 878 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} 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: 2.88, per 1000 atoms: 0.90 Number of scatterers: 3192 At special positions: 0 Unit cell: (77.72, 67.28, 98.6, 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 17 16.00 O 617 8.00 N 528 7.00 C 2030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 601 " - " ASN A 343 " Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 587.7 milliseconds 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 11.1% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'L' and resid 48 through 52 removed outlier: 3.810A pdb=" N ASN L 52 " --> pdb=" O ASP L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358 removed outlier: 4.100A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.734A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 46 through 48 removed outlier: 3.607A pdb=" N GLY H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL H 37 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN H 39 " --> pdb=" O LYS H 92 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS H 92 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR H 105 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 3 through 5 removed outlier: 3.771A pdb=" N VAL L 19 " --> pdb=" O ILE L 74 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE L 74 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET L 21 " --> pdb=" O LEU L 72 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU L 72 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS L 23 " --> pdb=" O TYR L 70 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR L 71 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER L 62 " --> pdb=" O THR L 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 45 through 47 removed outlier: 4.688A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN L 88 " --> pdb=" O TYR L 33 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR L 35 " --> pdb=" O TYR L 86 " (cutoff:3.500A) 72 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: 0.73 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1009 1.34 - 1.46: 881 1.46 - 1.58: 1364 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 3276 Sorted by residual: bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.426 -0.020 2.00e-02 2.50e+03 1.05e+00 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.65e-01 bond pdb=" CA MET L 77 " pdb=" CB MET L 77 " ideal model delta sigma weight residual 1.513 1.536 -0.023 2.59e-02 1.49e+03 7.75e-01 bond pdb=" C2 NAG A 601 " pdb=" N2 NAG A 601 " ideal model delta sigma weight residual 1.439 1.454 -0.015 2.00e-02 2.50e+03 5.78e-01 ... (remaining 3271 not shown) Histogram of bond angle deviations from ideal: 100.11 - 106.89: 103 106.89 - 113.66: 1679 113.66 - 120.44: 1220 120.44 - 127.22: 1417 127.22 - 134.00: 38 Bond angle restraints: 4457 Sorted by residual: angle pdb=" C ARG L 76 " pdb=" N MET L 77 " pdb=" CA MET L 77 " ideal model delta sigma weight residual 122.04 130.76 -8.72 2.11e+00 2.25e-01 1.71e+01 angle pdb=" CA ARG L 60 " pdb=" CB ARG L 60 " pdb=" CG ARG L 60 " ideal model delta sigma weight residual 114.10 121.10 -7.00 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA LEU H 29 " pdb=" CB LEU H 29 " pdb=" CG LEU H 29 " ideal model delta sigma weight residual 116.30 126.93 -10.63 3.50e+00 8.16e-02 9.23e+00 angle pdb=" C LEU H 67 " pdb=" N SER H 68 " pdb=" CA SER H 68 " ideal model delta sigma weight residual 121.62 126.42 -4.80 1.83e+00 2.99e-01 6.87e+00 angle pdb=" C GLY L 65 " pdb=" N CYS L 66 " pdb=" CA CYS L 66 " ideal model delta sigma weight residual 122.59 126.34 -3.75 1.57e+00 4.06e-01 5.70e+00 ... (remaining 4452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 1753 17.71 - 35.41: 159 35.41 - 53.12: 21 53.12 - 70.82: 0 70.82 - 88.53: 2 Dihedral angle restraints: 1935 sinusoidal: 758 harmonic: 1177 Sorted by residual: dihedral pdb=" CA MET L 77 " pdb=" C MET L 77 " pdb=" N GLU L 78 " pdb=" CA GLU L 78 " ideal model delta harmonic sigma weight residual -180.00 -152.03 -27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA TYR H 59 " pdb=" C TYR H 59 " pdb=" N ASN H 60 " pdb=" CA ASN H 60 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ASP L 81 " pdb=" C ASP L 81 " pdb=" N ALA L 82 " pdb=" CA ALA L 82 " ideal model delta harmonic sigma weight residual -180.00 -152.57 -27.43 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 1932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 312 0.037 - 0.074: 113 0.074 - 0.111: 37 0.111 - 0.147: 16 0.147 - 0.184: 2 Chirality restraints: 480 Sorted by residual: chirality pdb=" CB ILE A 402 " pdb=" CA ILE A 402 " pdb=" CG1 ILE A 402 " pdb=" CG2 ILE A 402 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CA ILE L 74 " pdb=" N ILE L 74 " pdb=" C ILE L 74 " pdb=" CB ILE L 74 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE L 47 " pdb=" N ILE L 47 " pdb=" C ILE L 47 " pdb=" CB ILE L 47 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 477 not shown) Planarity restraints: 573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 490 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO A 491 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.018 2.00e-02 2.50e+03 1.74e-02 3.80e+00 pdb=" CG ASN A 343 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.019 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 466 " -0.137 9.50e-02 1.11e+02 6.17e-02 2.96e+00 pdb=" NE ARG A 466 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 466 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 466 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 466 " -0.000 2.00e-02 2.50e+03 ... (remaining 570 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 130 2.72 - 3.27: 3159 3.27 - 3.81: 4603 3.81 - 4.36: 5272 4.36 - 4.90: 9289 Nonbonded interactions: 22453 Sorted by model distance: nonbonded pdb=" O SER H 7 " pdb=" OG1 THR H 21 " model vdw 2.177 3.040 nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.274 3.040 nonbonded pdb=" O ASN A 440 " pdb=" ND2 ASN L 91 " model vdw 2.324 3.120 nonbonded pdb=" O ALA A 475 " pdb=" ND2 ASN A 487 " model vdw 2.382 3.120 nonbonded pdb=" OG1 THR A 393 " pdb=" O HIS A 519 " model vdw 2.394 3.040 ... (remaining 22448 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.100 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5718 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3276 Z= 0.171 Angle : 0.795 10.631 4457 Z= 0.432 Chirality : 0.047 0.184 480 Planarity : 0.006 0.062 572 Dihedral : 13.042 88.529 1176 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.30 (0.38), residues: 400 helix: -3.71 (0.45), residues: 32 sheet: 2.48 (0.49), residues: 100 loop : -2.02 (0.31), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 PHE 0.015 0.002 PHE A 429 TYR 0.018 0.003 TYR L 85 ARG 0.014 0.002 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.318 Fit side-chains REVERT: A 486 PHE cc_start: 0.6384 (t80) cc_final: 0.6143 (t80) REVERT: L 34 TRP cc_start: 0.4286 (m100) cc_final: 0.4080 (m100) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1637 time to fit residues: 11.9295 Evaluate side-chains 53 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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: 0.4980 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.0050 chunk 15 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN L 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5685 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3276 Z= 0.183 Angle : 0.712 8.035 4457 Z= 0.386 Chirality : 0.046 0.253 480 Planarity : 0.005 0.055 572 Dihedral : 7.501 26.191 471 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.15 % Allowed : 10.34 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.39), residues: 400 helix: -2.22 (0.89), residues: 26 sheet: 1.56 (0.45), residues: 113 loop : -1.75 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 436 HIS 0.001 0.001 HIS H 35 PHE 0.029 0.002 PHE A 400 TYR 0.026 0.002 TYR A 423 ARG 0.002 0.000 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.307 Fit side-chains REVERT: A 365 TYR cc_start: 0.5710 (m-80) cc_final: 0.5444 (m-80) REVERT: A 410 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8086 (mm) REVERT: A 465 GLU cc_start: 0.6073 (tp30) cc_final: 0.5830 (tp30) REVERT: A 466 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7107 (mtm-85) REVERT: L 68 THR cc_start: 0.7002 (OUTLIER) cc_final: 0.6800 (m) outliers start: 4 outliers final: 2 residues processed: 56 average time/residue: 0.1718 time to fit residues: 11.6054 Evaluate side-chains 55 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain L residue 68 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.0020 chunk 10 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.0070 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 overall best weight: 0.3406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN H 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5731 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3276 Z= 0.175 Angle : 0.666 8.424 4457 Z= 0.360 Chirality : 0.046 0.284 480 Planarity : 0.005 0.051 572 Dihedral : 6.816 27.623 471 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.59 % Allowed : 12.36 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.19 (0.39), residues: 400 helix: -1.75 (1.05), residues: 26 sheet: 1.14 (0.45), residues: 115 loop : -1.74 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 36 HIS 0.001 0.000 HIS A 519 PHE 0.020 0.002 PHE A 486 TYR 0.012 0.002 TYR A 451 ARG 0.003 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.314 Fit side-chains REVERT: A 365 TYR cc_start: 0.5684 (m-80) cc_final: 0.5426 (m-80) REVERT: A 410 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8095 (mm) REVERT: L 68 THR cc_start: 0.6670 (m) cc_final: 0.6399 (m) outliers start: 9 outliers final: 3 residues processed: 59 average time/residue: 0.1614 time to fit residues: 11.5289 Evaluate side-chains 54 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain L residue 32 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.2980 chunk 3 optimal weight: 0.0050 chunk 16 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5699 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3276 Z= 0.161 Angle : 0.636 8.383 4457 Z= 0.343 Chirality : 0.045 0.246 480 Planarity : 0.004 0.047 572 Dihedral : 6.398 27.235 471 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.01 % Allowed : 13.79 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.37 (0.39), residues: 400 helix: -1.68 (1.04), residues: 26 sheet: 0.67 (0.44), residues: 115 loop : -1.68 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.011 0.001 PHE A 400 TYR 0.010 0.001 TYR A 453 ARG 0.001 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.375 Fit side-chains REVERT: A 365 TYR cc_start: 0.5645 (m-80) cc_final: 0.5374 (m-80) REVERT: A 410 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8050 (mm) REVERT: A 465 GLU cc_start: 0.6008 (tp30) cc_final: 0.5807 (tp30) REVERT: L 68 THR cc_start: 0.6678 (OUTLIER) cc_final: 0.6434 (m) outliers start: 7 outliers final: 2 residues processed: 50 average time/residue: 0.1725 time to fit residues: 10.5268 Evaluate side-chains 52 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 68 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 32 optimal weight: 0.0980 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.0470 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5692 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3276 Z= 0.152 Angle : 0.604 8.325 4457 Z= 0.328 Chirality : 0.044 0.218 480 Planarity : 0.004 0.047 572 Dihedral : 6.108 27.372 471 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.30 % Allowed : 14.94 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.39), residues: 400 helix: -1.70 (1.03), residues: 26 sheet: 0.51 (0.48), residues: 103 loop : -1.71 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 36 HIS 0.001 0.000 HIS H 35 PHE 0.022 0.002 PHE A 486 TYR 0.010 0.001 TYR A 423 ARG 0.001 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.361 Fit side-chains REVERT: A 408 ARG cc_start: 0.7570 (ptt90) cc_final: 0.7355 (ptt90) REVERT: A 410 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8028 (mm) outliers start: 8 outliers final: 4 residues processed: 53 average time/residue: 0.1663 time to fit residues: 10.7464 Evaluate side-chains 51 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 32 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 19 optimal weight: 0.0070 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN L 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5722 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3276 Z= 0.172 Angle : 0.645 8.485 4457 Z= 0.348 Chirality : 0.044 0.209 480 Planarity : 0.004 0.048 572 Dihedral : 6.055 26.992 471 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.72 % Allowed : 17.53 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.69 (0.38), residues: 400 helix: -1.91 (1.00), residues: 27 sheet: 0.62 (0.48), residues: 99 loop : -1.84 (0.33), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 36 HIS 0.001 0.001 HIS H 35 PHE 0.009 0.002 PHE A 400 TYR 0.012 0.001 TYR A 421 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.342 Fit side-chains REVERT: A 408 ARG cc_start: 0.7605 (ptt90) cc_final: 0.7395 (ptt90) REVERT: A 410 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7988 (mm) outliers start: 6 outliers final: 2 residues processed: 53 average time/residue: 0.1667 time to fit residues: 10.7874 Evaluate side-chains 54 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.0470 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.0170 chunk 11 optimal weight: 0.0170 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5746 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 0.021 3276 Z= 0.172 Angle : 0.645 8.365 4457 Z= 0.346 Chirality : 0.044 0.180 480 Planarity : 0.004 0.048 572 Dihedral : 6.048 26.895 471 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.15 % Allowed : 18.39 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.79 (0.39), residues: 400 helix: -1.86 (1.01), residues: 27 sheet: 0.41 (0.49), residues: 102 loop : -1.89 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 36 HIS 0.001 0.001 HIS H 35 PHE 0.009 0.002 PHE A 400 TYR 0.010 0.001 TYR H 58 ARG 0.001 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.345 Fit side-chains REVERT: A 408 ARG cc_start: 0.7615 (ptt90) cc_final: 0.7394 (ptt90) REVERT: A 410 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7969 (mm) REVERT: A 466 ARG cc_start: 0.7581 (mtm-85) cc_final: 0.7286 (mtm180) REVERT: A 509 ARG cc_start: 0.6425 (mtt180) cc_final: 0.5696 (mtp85) outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 0.1874 time to fit residues: 11.2555 Evaluate side-chains 51 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.0020 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5847 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3276 Z= 0.248 Angle : 0.718 8.465 4457 Z= 0.389 Chirality : 0.045 0.192 480 Planarity : 0.005 0.050 572 Dihedral : 6.358 26.945 471 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.15 % Allowed : 18.39 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.39), residues: 400 helix: -2.05 (0.99), residues: 27 sheet: 0.16 (0.50), residues: 106 loop : -1.96 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 36 HIS 0.002 0.001 HIS H 35 PHE 0.013 0.002 PHE A 497 TYR 0.016 0.002 TYR H 58 ARG 0.003 0.001 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.358 Fit side-chains REVERT: A 408 ARG cc_start: 0.7647 (ptt90) cc_final: 0.7446 (ptt90) REVERT: A 410 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8103 (mm) REVERT: A 509 ARG cc_start: 0.6524 (mtt180) cc_final: 0.5860 (mtp85) outliers start: 4 outliers final: 3 residues processed: 57 average time/residue: 0.1935 time to fit residues: 13.0348 Evaluate side-chains 55 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 37 optimal weight: 0.4980 chunk 22 optimal weight: 0.0970 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 38 optimal weight: 0.1980 chunk 35 optimal weight: 0.3980 chunk 30 optimal weight: 0.0170 chunk 3 optimal weight: 1.9990 overall best weight: 0.1614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5732 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3276 Z= 0.160 Angle : 0.651 8.108 4457 Z= 0.347 Chirality : 0.044 0.150 480 Planarity : 0.004 0.050 572 Dihedral : 5.845 26.240 471 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.86 % Allowed : 18.68 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.85 (0.40), residues: 400 helix: -1.79 (1.03), residues: 27 sheet: 0.35 (0.52), residues: 101 loop : -1.94 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 36 HIS 0.000 0.000 HIS H 35 PHE 0.013 0.001 PHE A 400 TYR 0.023 0.001 TYR L 35 ARG 0.002 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.347 Fit side-chains REVERT: A 408 ARG cc_start: 0.7589 (ptt90) cc_final: 0.7381 (ptt90) REVERT: A 410 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7780 (mm) outliers start: 3 outliers final: 1 residues processed: 48 average time/residue: 0.1696 time to fit residues: 9.9470 Evaluate side-chains 47 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain H residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.5338 > 50: distance: 27 - 32: 33.830 distance: 32 - 33: 42.418 distance: 33 - 34: 49.234 distance: 33 - 36: 48.362 distance: 34 - 35: 39.029 distance: 36 - 37: 39.202 distance: 38 - 39: 40.573 distance: 39 - 42: 56.270 distance: 40 - 41: 41.074 distance: 40 - 49: 53.472 distance: 42 - 43: 57.502 distance: 43 - 44: 38.949 distance: 43 - 45: 41.054 distance: 44 - 46: 68.649 distance: 45 - 47: 22.329 distance: 47 - 48: 58.019 distance: 49 - 50: 36.442 distance: 50 - 51: 26.336 distance: 50 - 53: 38.606 distance: 51 - 52: 36.527 distance: 51 - 57: 57.863 distance: 53 - 54: 55.784 distance: 53 - 55: 68.469 distance: 54 - 56: 57.365 distance: 57 - 58: 68.903 distance: 57 - 249: 37.429 distance: 58 - 61: 69.139 distance: 59 - 60: 39.037 distance: 61 - 62: 56.071 distance: 62 - 63: 39.676 distance: 62 - 64: 40.181 distance: 63 - 65: 39.698 distance: 65 - 67: 40.399 distance: 66 - 67: 55.806 distance: 67 - 68: 56.615 distance: 69 - 70: 41.037 distance: 69 - 167: 37.626 distance: 70 - 71: 40.955 distance: 70 - 73: 68.744 distance: 71 - 72: 40.202 distance: 71 - 83: 38.756 distance: 72 - 164: 32.317 distance: 73 - 74: 40.079 distance: 74 - 75: 13.958 distance: 74 - 76: 38.819 distance: 75 - 77: 46.627 distance: 76 - 78: 56.441 distance: 76 - 79: 41.344 distance: 77 - 78: 39.976 distance: 78 - 80: 39.071 distance: 79 - 81: 39.087 distance: 81 - 82: 40.184 distance: 83 - 84: 41.250 distance: 84 - 85: 56.315 distance: 84 - 87: 56.180 distance: 85 - 86: 40.137 distance: 85 - 95: 56.659 distance: 86 - 236: 32.733 distance: 88 - 89: 40.026 distance: 88 - 90: 42.063 distance: 89 - 91: 56.403 distance: 90 - 92: 49.568 distance: 91 - 93: 5.268 distance: 92 - 93: 53.403 distance: 93 - 94: 3.674 distance: 97 - 98: 41.100 distance: 97 - 104: 68.419 distance: 100 - 101: 22.820 distance: 101 - 102: 42.966 distance: 101 - 103: 23.131 distance: 105 - 106: 56.517 distance: 105 - 108: 40.316 distance: 106 - 107: 40.092 distance: 106 - 113: 40.377 distance: 109 - 110: 38.888 distance: 110 - 111: 39.290 distance: 110 - 112: 56.832 distance: 114 - 115: 69.995 distance: 114 - 117: 39.602 distance: 115 - 116: 55.607 distance: 117 - 118: 55.857 distance: 118 - 119: 57.178 distance: 119 - 120: 56.425 distance: 120 - 121: 56.114 distance: 122 - 123: 55.970 distance: 122 - 128: 41.257 distance: 123 - 124: 41.221 distance: 123 - 126: 40.836 distance: 124 - 129: 35.128 distance: 126 - 127: 56.874 distance: 127 - 128: 55.441