null Sun 23 Dec 22:22:56 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 2oc5-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oc5-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oc5-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc5-3.8-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/2oc5-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc5-3.8-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 ============================================================ Sun 23 Dec 22:23:06 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/2oc5-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc5-3.8-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 224 and 0 Target number of residues in the AU: 224 Target solvent content: 0.6539 Checking the provided sequence file Detected sequence length: 244 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 244 Adjusted target solvent content: 0.62 Input MTZ file: 2oc5-3.8-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: 96 Cell parameters: 77.390 77.390 116.960 90.000 90.000 90.000 Input sequence file: 2oc5-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1952 target number of atoms Had to go as low as 0.70 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.240 3.801 Wilson plot Bfac: 80.48 3791 reflections ( 99.03 % complete ) and 0 restraints for refining 2168 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3285 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3323 (Rfree = 0.000) for 2168 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 3.06 Search for helices and strands: 0 residues in 0 chains, 2246 seeds are put forward Round 1: 111 peptides, 20 chains. Longest chain 8 peptides. Score 0.338 Round 2: 136 peptides, 18 chains. Longest chain 15 peptides. Score 0.494 Round 3: 130 peptides, 16 chains. Longest chain 17 peptides. Score 0.507 Round 4: 136 peptides, 18 chains. Longest chain 15 peptides. Score 0.494 Round 5: 146 peptides, 15 chains. Longest chain 24 peptides. Score 0.587 Taking the results from Round 5 Chains 15, Residues 131, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3791 reflections ( 99.03 % complete ) and 3859 restraints for refining 1765 atoms. 3293 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2657 (Rfree = 0.000) for 1765 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 2: After refmac, R = 0.2449 (Rfree = 0.000) for 1724 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. Cycle 3: After refmac, R = 0.2490 (Rfree = 0.000) for 1692 atoms. Found 8 (9 requested) and removed 10 (4 requested) atoms. Cycle 4: After refmac, R = 0.2305 (Rfree = 0.000) for 1669 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 5: After refmac, R = 0.2181 (Rfree = 0.000) for 1657 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 3.06 Search for helices and strands: 0 residues in 0 chains, 1785 seeds are put forward Round 1: 130 peptides, 20 chains. Longest chain 12 peptides. Score 0.429 Round 2: 148 peptides, 19 chains. Longest chain 15 peptides. Score 0.524 Round 3: 149 peptides, 16 chains. Longest chain 24 peptides. Score 0.581 Round 4: 150 peptides, 18 chains. Longest chain 15 peptides. Score 0.550 Round 5: 148 peptides, 17 chains. Longest chain 22 peptides. Score 0.560 Taking the results from Round 3 Chains 16, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3791 reflections ( 99.03 % complete ) and 3713 restraints for refining 1720 atoms. 3197 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2663 (Rfree = 0.000) for 1720 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 7: After refmac, R = 0.2307 (Rfree = 0.000) for 1700 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 8: After refmac, R = 0.2234 (Rfree = 0.000) for 1683 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 9: After refmac, R = 0.2144 (Rfree = 0.000) for 1671 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 10: After refmac, R = 0.1961 (Rfree = 0.000) for 1669 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.05 Search for helices and strands: 0 residues in 0 chains, 1797 seeds are put forward Round 1: 138 peptides, 22 chains. Longest chain 14 peptides. Score 0.425 Round 2: 147 peptides, 19 chains. Longest chain 18 peptides. Score 0.521 Round 3: 141 peptides, 19 chains. Longest chain 17 peptides. Score 0.496 Round 4: 148 peptides, 21 chains. Longest chain 21 peptides. Score 0.488 Round 5: 143 peptides, 18 chains. Longest chain 15 peptides. Score 0.523 Taking the results from Round 5 Chains 18, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3791 reflections ( 99.03 % complete ) and 3999 restraints for refining 1763 atoms. 3517 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2678 (Rfree = 0.000) for 1763 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 12: After refmac, R = 0.2463 (Rfree = 0.000) for 1741 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 13: After refmac, R = 0.2398 (Rfree = 0.000) for 1718 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 14: After refmac, R = 0.2307 (Rfree = 0.000) for 1703 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 15: After refmac, R = 0.2298 (Rfree = 0.000) for 1691 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 3.00 Search for helices and strands: 0 residues in 0 chains, 1780 seeds are put forward Round 1: 118 peptides, 20 chains. Longest chain 10 peptides. Score 0.373 Round 2: 134 peptides, 20 chains. Longest chain 17 peptides. Score 0.447 Round 3: 145 peptides, 17 chains. Longest chain 25 peptides. Score 0.549 Round 4: 136 peptides, 17 chains. Longest chain 22 peptides. Score 0.513 Round 5: 139 peptides, 21 chains. Longest chain 15 peptides. Score 0.449 Taking the results from Round 3 Chains 18, Residues 128, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3791 reflections ( 99.03 % complete ) and 3787 restraints for refining 1764 atoms. 3241 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2559 (Rfree = 0.000) for 1764 atoms. Found 9 (9 requested) and removed 25 (4 requested) atoms. Cycle 17: After refmac, R = 0.2519 (Rfree = 0.000) for 1738 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 18: After refmac, R = 0.2379 (Rfree = 0.000) for 1721 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 19: After refmac, R = 0.2388 (Rfree = 0.000) for 1708 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 20: After refmac, R = 0.2254 (Rfree = 0.000) for 1699 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.59 3.05 Search for helices and strands: 0 residues in 0 chains, 1809 seeds are put forward Round 1: 130 peptides, 21 chains. Longest chain 12 peptides. Score 0.409 Round 2: 132 peptides, 17 chains. Longest chain 14 peptides. Score 0.497 Round 3: 139 peptides, 21 chains. Longest chain 12 peptides. Score 0.449 Round 4: 140 peptides, 19 chains. Longest chain 13 peptides. Score 0.492 Round 5: 139 peptides, 15 chains. Longest chain 21 peptides. Score 0.561 Taking the results from Round 5 Chains 15, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3791 reflections ( 99.03 % complete ) and 3837 restraints for refining 1764 atoms. 3356 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2670 (Rfree = 0.000) for 1764 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 22: After refmac, R = 0.2522 (Rfree = 0.000) for 1745 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 23: After refmac, R = 0.2601 (Rfree = 0.000) for 1729 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 24: After refmac, R = 0.2457 (Rfree = 0.000) for 1719 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 25: After refmac, R = 0.2452 (Rfree = 0.000) for 1710 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.02 Search for helices and strands: 0 residues in 0 chains, 1821 seeds are put forward Round 1: 120 peptides, 20 chains. Longest chain 12 peptides. Score 0.383 Round 2: 134 peptides, 19 chains. Longest chain 13 peptides. Score 0.466 Round 3: 130 peptides, 17 chains. Longest chain 16 peptides. Score 0.488 Round 4: 134 peptides, 20 chains. Longest chain 11 peptides. Score 0.447 Round 5: 128 peptides, 16 chains. Longest chain 13 peptides. Score 0.499 Taking the results from Round 5 Chains 16, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3791 reflections ( 99.03 % complete ) and 4051 restraints for refining 1765 atoms. 3619 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2777 (Rfree = 0.000) for 1765 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 27: After refmac, R = 0.2718 (Rfree = 0.000) for 1740 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 28: After refmac, R = 0.2649 (Rfree = 0.000) for 1714 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 29: After refmac, R = 0.2568 (Rfree = 0.000) for 1692 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 30: After refmac, R = 0.2647 (Rfree = 0.000) for 1674 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 3.09 Search for helices and strands: 0 residues in 0 chains, 1813 seeds are put forward Round 1: 109 peptides, 21 chains. Longest chain 9 peptides. Score 0.306 Round 2: 130 peptides, 24 chains. Longest chain 11 peptides. Score 0.347 Round 3: 134 peptides, 19 chains. Longest chain 17 peptides. Score 0.466 Round 4: 143 peptides, 23 chains. Longest chain 11 peptides. Score 0.428 Round 5: 135 peptides, 21 chains. Longest chain 12 peptides. Score 0.432 Taking the results from Round 3 Chains 19, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3791 reflections ( 99.03 % complete ) and 3751 restraints for refining 1712 atoms. 3310 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3060 (Rfree = 0.000) for 1712 atoms. Found 9 (9 requested) and removed 21 (4 requested) atoms. Cycle 32: After refmac, R = 0.3072 (Rfree = 0.000) for 1680 atoms. Found 9 (9 requested) and removed 21 (4 requested) atoms. Cycle 33: After refmac, R = 0.2608 (Rfree = 0.000) for 1648 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 34: After refmac, R = 0.3070 (Rfree = 0.000) for 1640 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 35: After refmac, R = 0.2601 (Rfree = 0.000) for 1623 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.66 3.11 Search for helices and strands: 0 residues in 0 chains, 1744 seeds are put forward Round 1: 96 peptides, 19 chains. Longest chain 8 peptides. Score 0.283 Round 2: 101 peptides, 15 chains. Longest chain 25 peptides. Score 0.399 Round 3: 115 peptides, 18 chains. Longest chain 12 peptides. Score 0.401 Round 4: 127 peptides, 18 chains. Longest chain 19 peptides. Score 0.456 Round 5: 126 peptides, 19 chains. Longest chain 14 peptides. Score 0.431 Taking the results from Round 4 Chains 18, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3791 reflections ( 99.03 % complete ) and 3630 restraints for refining 1659 atoms. 3212 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3236 (Rfree = 0.000) for 1659 atoms. Found 9 (9 requested) and removed 30 (4 requested) atoms. Cycle 37: After refmac, R = 0.2750 (Rfree = 0.000) for 1611 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 38: After refmac, R = 0.2608 (Rfree = 0.000) for 1590 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 39: After refmac, R = 0.2326 (Rfree = 0.000) for 1574 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 40: After refmac, R = 0.2685 (Rfree = 0.000) for 1570 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.12 Search for helices and strands: 0 residues in 0 chains, 1690 seeds are put forward Round 1: 97 peptides, 19 chains. Longest chain 9 peptides. Score 0.288 Round 2: 107 peptides, 16 chains. Longest chain 18 peptides. Score 0.405 Round 3: 116 peptides, 18 chains. Longest chain 13 peptides. Score 0.406 Round 4: 112 peptides, 16 chains. Longest chain 18 peptides. Score 0.429 Round 5: 117 peptides, 19 chains. Longest chain 11 peptides. Score 0.389 Taking the results from Round 4 Chains 16, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3791 reflections ( 99.03 % complete ) and 3883 restraints for refining 1726 atoms. 3515 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2912 (Rfree = 0.000) for 1726 atoms. Found 9 (9 requested) and removed 26 (4 requested) atoms. Cycle 42: After refmac, R = 0.3156 (Rfree = 0.000) for 1692 atoms. Found 9 (9 requested) and removed 34 (4 requested) atoms. Cycle 43: After refmac, R = 0.2463 (Rfree = 0.000) for 1643 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 44: After refmac, R = 0.2336 (Rfree = 0.000) for 1638 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.2373 (Rfree = 0.000) for 1639 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.05 Search for helices and strands: 0 residues in 0 chains, 1751 seeds are put forward Round 1: 95 peptides, 16 chains. Longest chain 12 peptides. Score 0.346 Round 2: 102 peptides, 17 chains. Longest chain 10 peptides. Score 0.359 Round 3: 109 peptides, 17 chains. Longest chain 20 peptides. Score 0.394 Round 4: 102 peptides, 16 chains. Longest chain 13 peptides. Score 0.381 Round 5: 110 peptides, 17 chains. Longest chain 21 peptides. Score 0.398 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 93, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2oc5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3791 reflections ( 99.03 % complete ) and 3867 restraints for refining 1717 atoms. 3472 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2849 (Rfree = 0.000) for 1717 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2825 (Rfree = 0.000) for 1702 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.3184 (Rfree = 0.000) for 1689 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2559 (Rfree = 0.000) for 1670 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:55:57 GMT 2018 Job finished. TimeTaking 33.03 Used memory is bytes: 14870216