Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ii1-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ii1-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ii1-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-3.4-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-3.4-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Tue 25 Dec 19:28:07 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-3.4-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 774 and 0 Target number of residues in the AU: 774 Target solvent content: 0.6227 Checking the provided sequence file Detected sequence length: 301 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1204 Adjusted target solvent content: 0.41 Input MTZ file: 2ii1-3.4-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 1 Cell parameters: 43.759 69.605 94.984 73.954 88.905 86.625 Input sequence file: 2ii1-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 9632 target number of atoms Had to go as low as 0.60 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 91.283 3.400 Wilson plot Bfac: 62.70 13485 reflections ( 91.19 % complete ) and 0 restraints for refining 10685 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3108 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2958 (Rfree = 0.000) for 10685 atoms. Found 68 (80 requested) and removed 396 (40 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 3.60 Search for helices and strands: 0 residues in 0 chains, 10421 seeds are put forward NCS extension: 0 residues added, 10421 seeds are put forward Round 1: 307 peptides, 66 chains. Longest chain 9 peptides. Score 0.245 Round 2: 383 peptides, 77 chains. Longest chain 8 peptides. Score 0.295 Round 3: 425 peptides, 80 chains. Longest chain 13 peptides. Score 0.342 Round 4: 421 peptides, 76 chains. Longest chain 11 peptides. Score 0.361 Round 5: 419 peptides, 74 chains. Longest chain 18 peptides. Score 0.371 Taking the results from Round 5 Chains 75, Residues 345, Estimated correctness of the model 0.0 % 12 chains (79 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 20130 restraints for refining 8758 atoms. 18602 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2356 (Rfree = 0.000) for 8758 atoms. Found 36 (66 requested) and removed 85 (33 requested) atoms. Cycle 2: After refmac, R = 0.2324 (Rfree = 0.000) for 8636 atoms. Found 39 (65 requested) and removed 60 (32 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.1954 (Rfree = 0.000) for 8576 atoms. Found 13 (65 requested) and removed 36 (32 requested) atoms. Cycle 4: After refmac, R = 0.1887 (Rfree = 0.000) for 8523 atoms. Found 11 (64 requested) and removed 38 (32 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.1887 (Rfree = 0.000) for 8479 atoms. Found 14 (64 requested) and removed 37 (32 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.61 Search for helices and strands: 0 residues in 0 chains, 8596 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 8609 seeds are put forward Round 1: 409 peptides, 85 chains. Longest chain 11 peptides. Score 0.283 Round 2: 505 peptides, 94 chains. Longest chain 13 peptides. Score 0.372 Round 3: 527 peptides, 96 chains. Longest chain 13 peptides. Score 0.392 Round 4: 522 peptides, 88 chains. Longest chain 16 peptides. Score 0.433 Round 5: 519 peptides, 88 chains. Longest chain 14 peptides. Score 0.429 Taking the results from Round 4 Chains 91, Residues 434, Estimated correctness of the model 0.0 % 15 chains (84 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 13485 reflections ( 91.19 % complete ) and 19218 restraints for refining 8502 atoms. 17368 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2146 (Rfree = 0.000) for 8502 atoms. Found 33 (64 requested) and removed 65 (32 requested) atoms. Cycle 7: After refmac, R = 0.2104 (Rfree = 0.000) for 8405 atoms. Found 27 (63 requested) and removed 40 (31 requested) atoms. Cycle 8: After refmac, R = 0.2030 (Rfree = 0.000) for 8361 atoms. Found 21 (63 requested) and removed 44 (31 requested) atoms. Cycle 9: After refmac, R = 0.1779 (Rfree = 0.000) for 8309 atoms. Found 10 (62 requested) and removed 38 (31 requested) atoms. Cycle 10: After refmac, R = 0.1734 (Rfree = 0.000) for 8265 atoms. Found 10 (62 requested) and removed 32 (31 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 3.59 Search for helices and strands: 0 residues in 0 chains, 8384 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 8397 seeds are put forward Round 1: 485 peptides, 94 chains. Longest chain 17 peptides. Score 0.343 Round 2: 506 peptides, 91 chains. Longest chain 13 peptides. Score 0.392 Round 3: 521 peptides, 90 chains. Longest chain 12 peptides. Score 0.419 Round 4: 510 peptides, 84 chains. Longest chain 19 peptides. Score 0.440 Round 5: 537 peptides, 91 chains. Longest chain 14 peptides. Score 0.436 Taking the results from Round 4 Chains 84, Residues 426, Estimated correctness of the model 0.0 % 11 chains (49 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 19288 restraints for refining 8406 atoms. 17543 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2088 (Rfree = 0.000) for 8406 atoms. Found 35 (63 requested) and removed 56 (31 requested) atoms. Cycle 12: After refmac, R = 0.2059 (Rfree = 0.000) for 8359 atoms. Found 35 (63 requested) and removed 39 (31 requested) atoms. Cycle 13: After refmac, R = 0.2052 (Rfree = 0.000) for 8344 atoms. Found 51 (63 requested) and removed 46 (31 requested) atoms. Cycle 14: After refmac, R = 0.1941 (Rfree = 0.000) for 8332 atoms. Found 39 (63 requested) and removed 43 (31 requested) atoms. Cycle 15: After refmac, R = 0.1676 (Rfree = 0.000) for 8316 atoms. Found 6 (62 requested) and removed 32 (31 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.19 3.60 Search for helices and strands: 0 residues in 0 chains, 8439 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 8454 seeds are put forward Round 1: 469 peptides, 98 chains. Longest chain 10 peptides. Score 0.293 Round 2: 510 peptides, 89 chains. Longest chain 14 peptides. Score 0.410 Round 3: 529 peptides, 92 chains. Longest chain 13 peptides. Score 0.419 Round 4: 545 peptides, 93 chains. Longest chain 21 peptides. Score 0.435 Round 5: 515 peptides, 85 chains. Longest chain 16 peptides. Score 0.441 Taking the results from Round 5 Chains 87, Residues 430, Estimated correctness of the model 0.0 % 7 chains (40 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 19971 restraints for refining 8626 atoms. 18236 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1861 (Rfree = 0.000) for 8626 atoms. Found 29 (65 requested) and removed 58 (32 requested) atoms. Cycle 17: After refmac, R = 0.1811 (Rfree = 0.000) for 8569 atoms. Found 28 (64 requested) and removed 40 (32 requested) atoms. Cycle 18: After refmac, R = 0.1727 (Rfree = 0.000) for 8538 atoms. Found 25 (64 requested) and removed 38 (32 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1717 (Rfree = 0.000) for 8515 atoms. Found 22 (64 requested) and removed 35 (32 requested) atoms. Cycle 20: After refmac, R = 0.1672 (Rfree = 0.000) for 8495 atoms. Found 28 (64 requested) and removed 38 (32 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 3.60 Search for helices and strands: 0 residues in 0 chains, 8646 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8661 seeds are put forward Round 1: 423 peptides, 89 chains. Longest chain 9 peptides. Score 0.279 Round 2: 485 peptides, 85 chains. Longest chain 16 peptides. Score 0.399 Round 3: 512 peptides, 88 chains. Longest chain 16 peptides. Score 0.419 Round 4: 498 peptides, 83 chains. Longest chain 18 peptides. Score 0.429 Round 5: 526 peptides, 81 chains. Longest chain 19 peptides. Score 0.479 Taking the results from Round 5 Chains 81, Residues 445, Estimated correctness of the model 0.0 % 6 chains (27 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 20192 restraints for refining 8737 atoms. 18437 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1825 (Rfree = 0.000) for 8737 atoms. Found 21 (65 requested) and removed 51 (32 requested) atoms. Cycle 22: After refmac, R = 0.1805 (Rfree = 0.000) for 8686 atoms. Found 35 (65 requested) and removed 39 (32 requested) atoms. Cycle 23: After refmac, R = 0.1835 (Rfree = 0.000) for 8668 atoms. Found 42 (65 requested) and removed 42 (32 requested) atoms. Cycle 24: After refmac, R = 0.1692 (Rfree = 0.000) for 8663 atoms. Found 20 (65 requested) and removed 40 (32 requested) atoms. Cycle 25: After refmac, R = 0.1638 (Rfree = 0.000) for 8636 atoms. Found 22 (65 requested) and removed 39 (32 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 3.58 Search for helices and strands: 0 residues in 0 chains, 8801 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 8814 seeds are put forward Round 1: 438 peptides, 88 chains. Longest chain 11 peptides. Score 0.309 Round 2: 504 peptides, 87 chains. Longest chain 16 peptides. Score 0.414 Round 3: 491 peptides, 82 chains. Longest chain 12 peptides. Score 0.426 Round 4: 503 peptides, 81 chains. Longest chain 20 peptides. Score 0.448 Round 5: 509 peptides, 81 chains. Longest chain 17 peptides. Score 0.456 Taking the results from Round 5 Chains 82, Residues 428, Estimated correctness of the model 0.0 % 6 chains (42 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 20261 restraints for refining 8758 atoms. 18523 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1747 (Rfree = 0.000) for 8758 atoms. Found 30 (66 requested) and removed 39 (33 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1666 (Rfree = 0.000) for 8728 atoms. Found 30 (66 requested) and removed 39 (33 requested) atoms. Cycle 28: After refmac, R = 0.1601 (Rfree = 0.000) for 8713 atoms. Found 31 (65 requested) and removed 36 (32 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1585 (Rfree = 0.000) for 8701 atoms. Found 20 (65 requested) and removed 34 (32 requested) atoms. Cycle 30: After refmac, R = 0.1547 (Rfree = 0.000) for 8678 atoms. Found 21 (65 requested) and removed 34 (32 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 3.59 Search for helices and strands: 0 residues in 0 chains, 8800 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8815 seeds are put forward Round 1: 408 peptides, 87 chains. Longest chain 11 peptides. Score 0.268 Round 2: 417 peptides, 75 chains. Longest chain 14 peptides. Score 0.362 Round 3: 450 peptides, 79 chains. Longest chain 17 peptides. Score 0.386 Round 4: 468 peptides, 81 chains. Longest chain 14 peptides. Score 0.399 Round 5: 483 peptides, 78 chains. Longest chain 17 peptides. Score 0.439 Taking the results from Round 5 Chains 79, Residues 405, Estimated correctness of the model 0.0 % 9 chains (54 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 20269 restraints for refining 8758 atoms. 18597 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1738 (Rfree = 0.000) for 8758 atoms. Found 30 (66 requested) and removed 40 (33 requested) atoms. Cycle 32: After refmac, R = 0.1712 (Rfree = 0.000) for 8716 atoms. Found 44 (66 requested) and removed 40 (33 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1670 (Rfree = 0.000) for 8712 atoms. Found 56 (65 requested) and removed 38 (32 requested) atoms. Cycle 34: After refmac, R = 0.1634 (Rfree = 0.000) for 8726 atoms. Found 37 (65 requested) and removed 33 (32 requested) atoms. Cycle 35: After refmac, R = 0.1582 (Rfree = 0.000) for 8724 atoms. Found 34 (65 requested) and removed 35 (32 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 3.59 Search for helices and strands: 0 residues in 0 chains, 8870 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 8889 seeds are put forward Round 1: 380 peptides, 82 chains. Longest chain 11 peptides. Score 0.256 Round 2: 426 peptides, 74 chains. Longest chain 12 peptides. Score 0.382 Round 3: 414 peptides, 75 chains. Longest chain 12 peptides. Score 0.357 Round 4: 420 peptides, 72 chains. Longest chain 15 peptides. Score 0.386 Round 5: 407 peptides, 69 chains. Longest chain 13 peptides. Score 0.386 Taking the results from Round 5 Chains 69, Residues 338, Estimated correctness of the model 0.0 % 7 chains (37 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 20908 restraints for refining 8757 atoms. 19539 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1727 (Rfree = 0.000) for 8757 atoms. Found 41 (66 requested) and removed 36 (33 requested) atoms. Cycle 37: After refmac, R = 0.1654 (Rfree = 0.000) for 8742 atoms. Found 34 (66 requested) and removed 35 (33 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1583 (Rfree = 0.000) for 8732 atoms. Found 33 (65 requested) and removed 32 (32 requested) atoms. Cycle 39: After refmac, R = 0.1551 (Rfree = 0.000) for 8725 atoms. Found 34 (65 requested) and removed 37 (32 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1546 (Rfree = 0.000) for 8716 atoms. Found 35 (65 requested) and removed 33 (32 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.58 Search for helices and strands: 0 residues in 0 chains, 8866 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 8885 seeds are put forward Round 1: 381 peptides, 84 chains. Longest chain 11 peptides. Score 0.244 Round 2: 425 peptides, 78 chains. Longest chain 12 peptides. Score 0.355 Round 3: 442 peptides, 79 chains. Longest chain 22 peptides. Score 0.374 Round 4: 417 peptides, 73 chains. Longest chain 14 peptides. Score 0.375 Round 5: 432 peptides, 71 chains. Longest chain 17 peptides. Score 0.410 Taking the results from Round 5 Chains 73, Residues 361, Estimated correctness of the model 0.0 % 6 chains (38 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 20681 restraints for refining 8757 atoms. 19217 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1687 (Rfree = 0.000) for 8757 atoms. Found 42 (66 requested) and removed 37 (33 requested) atoms. Cycle 42: After refmac, R = 0.1613 (Rfree = 0.000) for 8744 atoms. Found 27 (66 requested) and removed 38 (33 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1592 (Rfree = 0.000) for 8712 atoms. Found 38 (65 requested) and removed 35 (32 requested) atoms. Cycle 44: After refmac, R = 0.1571 (Rfree = 0.000) for 8700 atoms. Found 36 (65 requested) and removed 34 (32 requested) atoms. Cycle 45: After refmac, R = 0.1537 (Rfree = 0.000) for 8694 atoms. Found 28 (65 requested) and removed 33 (32 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 3.59 Search for helices and strands: 0 residues in 0 chains, 8837 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 8857 seeds are put forward Round 1: 363 peptides, 77 chains. Longest chain 11 peptides. Score 0.263 Round 2: 414 peptides, 73 chains. Longest chain 15 peptides. Score 0.370 Round 3: 421 peptides, 77 chains. Longest chain 17 peptides. Score 0.355 Round 4: 430 peptides, 73 chains. Longest chain 19 peptides. Score 0.394 Round 5: 426 peptides, 74 chains. Longest chain 15 peptides. Score 0.382 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 74, Residues 357, Estimated correctness of the model 0.0 % 7 chains (38 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2ii1-3_warpNtrace.pdb as input Building loops using Loopy2018 74 chains (357 residues) following loop building 7 chains (38 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13485 reflections ( 91.19 % complete ) and 20652 restraints for refining 8756 atoms. 19211 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1655 (Rfree = 0.000) for 8756 atoms. Found 0 (66 requested) and removed 33 (33 requested) atoms. Cycle 47: After refmac, R = 0.1608 (Rfree = 0.000) for 8704 atoms. Found 0 (65 requested) and removed 32 (32 requested) atoms. Cycle 48: After refmac, R = 0.1566 (Rfree = 0.000) for 8665 atoms. Found 0 (65 requested) and removed 32 (32 requested) atoms. Cycle 49: After refmac, R = 0.1523 (Rfree = 0.000) for 8627 atoms. Found 0 (65 requested) and removed 32 (32 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:20:27 GMT 2018 Job finished. Failed to save intermediate PDB TimeTaking 112.5