null Tue 25 Dec 19:27:56 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 2awa-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2awa-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2awa-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2awa-4.0-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/2awa-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2awa-4.0-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 19:28:11 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/2awa-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2awa-4.0-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 1114 and 0 Target number of residues in the AU: 1114 Target solvent content: 0.6673 Checking the provided sequence file Detected sequence length: 390 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1560 Adjusted target solvent content: 0.53 Input MTZ file: 2awa-4.0-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: 4 Cell parameters: 94.281 70.854 135.686 90.000 91.232 90.000 Input sequence file: 2awa-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 12480 target number of atoms Had to go as low as 0.85 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: 135.654 4.000 Wilson plot Bfac: 90.32 14641 reflections ( 94.66 % complete ) and 0 restraints for refining 13849 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3516 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3208 (Rfree = 0.000) for 13849 atoms. Found 65 (65 requested) and removed 92 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.84 3.69 Search for helices and strands: 0 residues in 0 chains, 13989 seeds are put forward NCS extension: 0 residues added, 13989 seeds are put forward Round 1: 382 peptides, 83 chains. Longest chain 11 peptides. Score 0.228 Round 2: 508 peptides, 94 chains. Longest chain 11 peptides. Score 0.314 Round 3: 584 peptides, 104 chains. Longest chain 13 peptides. Score 0.346 Round 4: 633 peptides, 108 chains. Longest chain 23 peptides. Score 0.376 Round 5: 624 peptides, 106 chains. Longest chain 15 peptides. Score 0.375 Taking the results from Round 4 Chains 108, Residues 525, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14641 reflections ( 94.66 % complete ) and 27634 restraints for refining 11267 atoms. 25642 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2554 (Rfree = 0.000) for 11267 atoms. Found 38 (53 requested) and removed 64 (26 requested) atoms. Cycle 2: After refmac, R = 0.2390 (Rfree = 0.000) for 11066 atoms. Found 33 (53 requested) and removed 74 (26 requested) atoms. Cycle 3: After refmac, R = 0.1934 (Rfree = 0.000) for 10930 atoms. Found 12 (52 requested) and removed 43 (26 requested) atoms. Cycle 4: After refmac, R = 0.1830 (Rfree = 0.000) for 10845 atoms. Found 9 (51 requested) and removed 39 (25 requested) atoms. Cycle 5: After refmac, R = 0.2232 (Rfree = 0.000) for 10782 atoms. Found 51 (51 requested) and removed 59 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.78 3.63 Search for helices and strands: 0 residues in 0 chains, 11058 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 11074 seeds are put forward Round 1: 563 peptides, 113 chains. Longest chain 11 peptides. Score 0.287 Round 2: 645 peptides, 109 chains. Longest chain 21 peptides. Score 0.383 Round 3: 671 peptides, 108 chains. Longest chain 21 peptides. Score 0.410 Round 4: 695 peptides, 107 chains. Longest chain 21 peptides. Score 0.435 Round 5: 704 peptides, 109 chains. Longest chain 21 peptides. Score 0.435 Taking the results from Round 5 Chains 111, Residues 595, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 14641 reflections ( 94.66 % complete ) and 26135 restraints for refining 11133 atoms. 23771 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2371 (Rfree = 0.000) for 11133 atoms. Found 42 (52 requested) and removed 81 (26 requested) atoms. Cycle 7: After refmac, R = 0.2235 (Rfree = 0.000) for 10968 atoms. Found 42 (52 requested) and removed 64 (26 requested) atoms. Cycle 8: After refmac, R = 0.2213 (Rfree = 0.000) for 10850 atoms. Found 38 (52 requested) and removed 64 (26 requested) atoms. Cycle 9: After refmac, R = 0.1705 (Rfree = 0.000) for 10773 atoms. Found 9 (51 requested) and removed 39 (25 requested) atoms. Cycle 10: After refmac, R = 0.1620 (Rfree = 0.000) for 10715 atoms. Found 14 (51 requested) and removed 35 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.83 3.68 Search for helices and strands: 0 residues in 0 chains, 10926 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 10944 seeds are put forward Round 1: 613 peptides, 122 chains. Longest chain 13 peptides. Score 0.299 Round 2: 701 peptides, 120 chains. Longest chain 14 peptides. Score 0.390 Round 3: 669 peptides, 113 chains. Longest chain 23 peptides. Score 0.389 Round 4: 707 peptides, 112 chains. Longest chain 16 peptides. Score 0.426 Round 5: 699 peptides, 108 chains. Longest chain 19 peptides. Score 0.435 Taking the results from Round 5 Chains 108, Residues 591, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14641 reflections ( 94.66 % complete ) and 26246 restraints for refining 11270 atoms. 23990 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2328 (Rfree = 0.000) for 11270 atoms. Found 45 (53 requested) and removed 91 (26 requested) atoms. Cycle 12: After refmac, R = 0.2222 (Rfree = 0.000) for 11139 atoms. Found 53 (53 requested) and removed 77 (26 requested) atoms. Cycle 13: After refmac, R = 0.2122 (Rfree = 0.000) for 11054 atoms. Found 52 (52 requested) and removed 54 (26 requested) atoms. Cycle 14: After refmac, R = 0.1725 (Rfree = 0.000) for 10995 atoms. Found 15 (52 requested) and removed 46 (26 requested) atoms. Cycle 15: After refmac, R = 0.1667 (Rfree = 0.000) for 10936 atoms. Found 18 (52 requested) and removed 41 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.83 3.68 Search for helices and strands: 0 residues in 0 chains, 11172 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 11185 seeds are put forward Round 1: 626 peptides, 121 chains. Longest chain 14 peptides. Score 0.316 Round 2: 670 peptides, 115 chains. Longest chain 15 peptides. Score 0.382 Round 3: 690 peptides, 116 chains. Longest chain 14 peptides. Score 0.396 Round 4: 688 peptides, 115 chains. Longest chain 13 peptides. Score 0.398 Round 5: 709 peptides, 108 chains. Longest chain 18 peptides. Score 0.443 Taking the results from Round 5 Chains 108, Residues 601, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14641 reflections ( 94.66 % complete ) and 26645 restraints for refining 11268 atoms. 24349 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2360 (Rfree = 0.000) for 11268 atoms. Found 53 (53 requested) and removed 54 (26 requested) atoms. Cycle 17: After refmac, R = 0.2241 (Rfree = 0.000) for 11188 atoms. Found 53 (53 requested) and removed 64 (26 requested) atoms. Cycle 18: After refmac, R = 0.2100 (Rfree = 0.000) for 11115 atoms. Found 38 (53 requested) and removed 53 (26 requested) atoms. Cycle 19: After refmac, R = 0.1673 (Rfree = 0.000) for 11049 atoms. Found 4 (52 requested) and removed 36 (26 requested) atoms. Cycle 20: After refmac, R = 0.1606 (Rfree = 0.000) for 10985 atoms. Found 13 (52 requested) and removed 36 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.81 3.66 Search for helices and strands: 0 residues in 0 chains, 11226 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 11248 seeds are put forward Round 1: 608 peptides, 117 chains. Longest chain 11 peptides. Score 0.315 Round 2: 672 peptides, 110 chains. Longest chain 18 peptides. Score 0.403 Round 3: 671 peptides, 104 chains. Longest chain 19 peptides. Score 0.426 Round 4: 650 peptides, 97 chains. Longest chain 17 peptides. Score 0.435 Round 5: 637 peptides, 103 chains. Longest chain 13 peptides. Score 0.399 Taking the results from Round 4 Chains 97, Residues 553, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14641 reflections ( 94.66 % complete ) and 26805 restraints for refining 11267 atoms. 24690 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2107 (Rfree = 0.000) for 11267 atoms. Found 52 (53 requested) and removed 45 (26 requested) atoms. Cycle 22: After refmac, R = 0.2134 (Rfree = 0.000) for 11194 atoms. Found 52 (53 requested) and removed 43 (26 requested) atoms. Cycle 23: After refmac, R = 0.2044 (Rfree = 0.000) for 11170 atoms. Found 49 (53 requested) and removed 50 (26 requested) atoms. Cycle 24: After refmac, R = 0.2004 (Rfree = 0.000) for 11138 atoms. Found 53 (53 requested) and removed 46 (26 requested) atoms. Cycle 25: After refmac, R = 0.1940 (Rfree = 0.000) for 11113 atoms. Found 49 (52 requested) and removed 46 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.79 3.64 Search for helices and strands: 0 residues in 0 chains, 11345 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 11369 seeds are put forward Round 1: 535 peptides, 109 chains. Longest chain 11 peptides. Score 0.275 Round 2: 619 peptides, 109 chains. Longest chain 17 peptides. Score 0.358 Round 3: 629 peptides, 111 chains. Longest chain 15 peptides. Score 0.360 Round 4: 622 peptides, 106 chains. Longest chain 14 peptides. Score 0.373 Round 5: 632 peptides, 106 chains. Longest chain 15 peptides. Score 0.383 Taking the results from Round 5 Chains 106, Residues 526, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14641 reflections ( 94.66 % complete ) and 26869 restraints for refining 11268 atoms. 24871 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2051 (Rfree = 0.000) for 11268 atoms. Found 46 (53 requested) and removed 48 (26 requested) atoms. Cycle 27: After refmac, R = 0.1911 (Rfree = 0.000) for 11162 atoms. Found 50 (53 requested) and removed 41 (26 requested) atoms. Cycle 28: After refmac, R = 0.1797 (Rfree = 0.000) for 11126 atoms. Found 52 (53 requested) and removed 36 (26 requested) atoms. Cycle 29: After refmac, R = 0.1492 (Rfree = 0.000) for 11098 atoms. Found 12 (52 requested) and removed 38 (26 requested) atoms. Cycle 30: After refmac, R = 0.1433 (Rfree = 0.000) for 11050 atoms. Found 8 (52 requested) and removed 30 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.81 3.66 Search for helices and strands: 0 residues in 0 chains, 11266 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 11279 seeds are put forward Round 1: 510 peptides, 112 chains. Longest chain 9 peptides. Score 0.236 Round 2: 575 peptides, 111 chains. Longest chain 13 peptides. Score 0.307 Round 3: 586 peptides, 108 chains. Longest chain 13 peptides. Score 0.331 Round 4: 591 peptides, 105 chains. Longest chain 13 peptides. Score 0.348 Round 5: 616 peptides, 105 chains. Longest chain 15 peptides. Score 0.372 Taking the results from Round 5 Chains 105, Residues 511, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14641 reflections ( 94.66 % complete ) and 26774 restraints for refining 11268 atoms. 24835 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2002 (Rfree = 0.000) for 11268 atoms. Found 50 (53 requested) and removed 58 (26 requested) atoms. Cycle 32: After refmac, R = 0.1938 (Rfree = 0.000) for 11200 atoms. Found 53 (53 requested) and removed 44 (26 requested) atoms. Cycle 33: After refmac, R = 0.1907 (Rfree = 0.000) for 11160 atoms. Found 53 (53 requested) and removed 49 (26 requested) atoms. Cycle 34: After refmac, R = 0.1787 (Rfree = 0.000) for 11127 atoms. Found 53 (53 requested) and removed 43 (26 requested) atoms. Cycle 35: After refmac, R = 0.1405 (Rfree = 0.000) for 11116 atoms. Found 6 (52 requested) and removed 37 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.77 3.62 Search for helices and strands: 0 residues in 0 chains, 11288 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 11311 seeds are put forward Round 1: 468 peptides, 103 chains. Longest chain 10 peptides. Score 0.231 Round 2: 532 peptides, 103 chains. Longest chain 13 peptides. Score 0.299 Round 3: 545 peptides, 100 chains. Longest chain 14 peptides. Score 0.325 Round 4: 552 peptides, 96 chains. Longest chain 15 peptides. Score 0.349 Round 5: 543 peptides, 100 chains. Longest chain 18 peptides. Score 0.323 Taking the results from Round 4 Chains 96, Residues 456, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14641 reflections ( 94.66 % complete ) and 26954 restraints for refining 11259 atoms. 25226 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1944 (Rfree = 0.000) for 11259 atoms. Found 44 (53 requested) and removed 73 (26 requested) atoms. Cycle 37: After refmac, R = 0.1873 (Rfree = 0.000) for 11168 atoms. Found 53 (53 requested) and removed 57 (26 requested) atoms. Cycle 38: After refmac, R = 0.1513 (Rfree = 0.000) for 11114 atoms. Found 10 (53 requested) and removed 38 (26 requested) atoms. Cycle 39: After refmac, R = 0.1435 (Rfree = 0.000) for 11066 atoms. Found 10 (52 requested) and removed 30 (26 requested) atoms. Cycle 40: After refmac, R = 0.1434 (Rfree = 0.000) for 11036 atoms. Found 10 (52 requested) and removed 39 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.80 3.65 Search for helices and strands: 0 residues in 0 chains, 11205 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 11225 seeds are put forward Round 1: 435 peptides, 98 chains. Longest chain 7 peptides. Score 0.217 Round 2: 488 peptides, 94 chains. Longest chain 17 peptides. Score 0.293 Round 3: 523 peptides, 97 chains. Longest chain 17 peptides. Score 0.316 Round 4: 508 peptides, 90 chains. Longest chain 16 peptides. Score 0.331 Round 5: 528 peptides, 94 chains. Longest chain 23 peptides. Score 0.334 Taking the results from Round 5 Chains 94, Residues 434, Estimated correctness of the model 0.0 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 14641 reflections ( 94.66 % complete ) and 26652 restraints for refining 11269 atoms. 24908 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1874 (Rfree = 0.000) for 11269 atoms. Found 50 (53 requested) and removed 67 (26 requested) atoms. Cycle 42: After refmac, R = 0.1914 (Rfree = 0.000) for 11221 atoms. Found 53 (53 requested) and removed 54 (26 requested) atoms. Cycle 43: After refmac, R = 0.1819 (Rfree = 0.000) for 11197 atoms. Found 53 (53 requested) and removed 46 (26 requested) atoms. Cycle 44: After refmac, R = 0.1459 (Rfree = 0.000) for 11174 atoms. Found 7 (53 requested) and removed 32 (26 requested) atoms. Cycle 45: After refmac, R = 0.1387 (Rfree = 0.000) for 11126 atoms. Found 8 (52 requested) and removed 30 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.79 3.64 Search for helices and strands: 0 residues in 0 chains, 11286 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 11320 seeds are put forward Round 1: 389 peptides, 88 chains. Longest chain 9 peptides. Score 0.212 Round 2: 457 peptides, 90 chains. Longest chain 11 peptides. Score 0.278 Round 3: 435 peptides, 87 chains. Longest chain 13 peptides. Score 0.269 Round 4: 426 peptides, 81 chains. Longest chain 14 peptides. Score 0.287 Round 5: 428 peptides, 81 chains. Longest chain 14 peptides. Score 0.289 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 81, Residues 347, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2awa-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14641 reflections ( 94.66 % complete ) and 27711 restraints for refining 11268 atoms. 26404 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1987 (Rfree = 0.000) for 11268 atoms. Found 0 (53 requested) and removed 26 (26 requested) atoms. Cycle 47: After refmac, R = 0.2002 (Rfree = 0.000) for 11210 atoms. Found 0 (53 requested) and removed 26 (26 requested) atoms. Cycle 48: After refmac, R = 0.1932 (Rfree = 0.000) for 11150 atoms. Found 0 (53 requested) and removed 26 (26 requested) atoms. Cycle 49: After refmac, R = 0.1948 (Rfree = 0.000) for 11092 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 22:07:05 GMT 2018 Job finished. TimeTaking 159.15 Used memory is bytes: 16972392