null Mon 24 Dec 00:53:07 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2hx1-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2hx1-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2hx1-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.4-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:53:12 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/mrncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.4-parrot-mrncs/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 868 and 0 Target number of residues in the AU: 868 Target solvent content: 0.6039 Checking the provided sequence file Detected sequence length: 284 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1136 Adjusted target solvent content: 0.48 Input MTZ file: 2hx1-3.4-parrot-mrncs.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: 19 Cell parameters: 65.624 119.462 151.274 90.000 90.000 90.000 Input sequence file: 2hx1-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 9088 target number of atoms Had to go as low as 0.75 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: 93.753 3.400 Wilson plot Bfac: 54.11 16942 reflections ( 99.75 % complete ) and 0 restraints for refining 10132 atoms. Observations/parameters ratio is 0.42 ------------------------------------------------------ Starting model: R = 0.3228 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2967 (Rfree = 0.000) for 10132 atoms. Found 76 (76 requested) and removed 74 (38 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.12 3.20 Search for helices and strands: 0 residues in 0 chains, 10331 seeds are put forward NCS extension: 0 residues added, 10331 seeds are put forward Round 1: 522 peptides, 101 chains. Longest chain 11 peptides. Score 0.345 Round 2: 660 peptides, 98 chains. Longest chain 27 peptides. Score 0.535 Round 3: 731 peptides, 103 chains. Longest chain 18 peptides. Score 0.587 Round 4: 767 peptides, 99 chains. Longest chain 29 peptides. Score 0.638 Round 5: 795 peptides, 94 chains. Longest chain 22 peptides. Score 0.682 Taking the results from Round 5 Chains 97, Residues 701, Estimated correctness of the model 53.1 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 17465 restraints for refining 8261 atoms. 14614 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2708 (Rfree = 0.000) for 8261 atoms. Found 57 (62 requested) and removed 58 (31 requested) atoms. Cycle 2: After refmac, R = 0.2521 (Rfree = 0.000) for 8151 atoms. Found 43 (62 requested) and removed 50 (31 requested) atoms. Cycle 3: After refmac, R = 0.2408 (Rfree = 0.000) for 8095 atoms. Found 23 (61 requested) and removed 41 (30 requested) atoms. Cycle 4: After refmac, R = 0.2332 (Rfree = 0.000) for 8049 atoms. Found 31 (60 requested) and removed 39 (30 requested) atoms. Cycle 5: After refmac, R = 0.2321 (Rfree = 0.000) for 8027 atoms. Found 28 (60 requested) and removed 42 (30 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 3.28 Search for helices and strands: 0 residues in 0 chains, 8308 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 8339 seeds are put forward Round 1: 693 peptides, 98 chains. Longest chain 20 peptides. Score 0.571 Round 2: 786 peptides, 89 chains. Longest chain 37 peptides. Score 0.693 Round 3: 777 peptides, 86 chains. Longest chain 31 peptides. Score 0.697 Round 4: 761 peptides, 88 chains. Longest chain 29 peptides. Score 0.676 Round 5: 786 peptides, 83 chains. Longest chain 27 peptides. Score 0.714 Taking the results from Round 5 Chains 84, Residues 703, Estimated correctness of the model 61.4 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 17840 restraints for refining 8263 atoms. 15044 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2656 (Rfree = 0.000) for 8263 atoms. Found 62 (62 requested) and removed 56 (31 requested) atoms. Cycle 7: After refmac, R = 0.2568 (Rfree = 0.000) for 8229 atoms. Found 41 (61 requested) and removed 49 (31 requested) atoms. Cycle 8: After refmac, R = 0.2435 (Rfree = 0.000) for 8198 atoms. Found 46 (60 requested) and removed 42 (31 requested) atoms. Cycle 9: After refmac, R = 0.2370 (Rfree = 0.000) for 8181 atoms. Found 37 (57 requested) and removed 40 (30 requested) atoms. Cycle 10: After refmac, R = 0.2254 (Rfree = 0.000) for 8163 atoms. Found 29 (56 requested) and removed 41 (30 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 8430 seeds are put forward NCS extension: 21 residues added (5 deleted due to clashes), 8451 seeds are put forward Round 1: 689 peptides, 96 chains. Longest chain 29 peptides. Score 0.576 Round 2: 746 peptides, 88 chains. Longest chain 27 peptides. Score 0.664 Round 3: 774 peptides, 87 chains. Longest chain 27 peptides. Score 0.691 Round 4: 766 peptides, 86 chains. Longest chain 36 peptides. Score 0.688 Round 5: 780 peptides, 95 chains. Longest chain 30 peptides. Score 0.666 Taking the results from Round 3 Chains 90, Residues 687, Estimated correctness of the model 55.5 % 3 chains (47 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 17727 restraints for refining 8261 atoms. 14896 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2515 (Rfree = 0.000) for 8261 atoms. Found 56 (56 requested) and removed 46 (31 requested) atoms. Cycle 12: After refmac, R = 0.2309 (Rfree = 0.000) for 8242 atoms. Found 40 (56 requested) and removed 43 (31 requested) atoms. Cycle 13: After refmac, R = 0.2312 (Rfree = 0.000) for 8210 atoms. Found 37 (56 requested) and removed 37 (31 requested) atoms. Cycle 14: After refmac, R = 0.2238 (Rfree = 0.000) for 8191 atoms. Found 34 (55 requested) and removed 32 (30 requested) atoms. Cycle 15: After refmac, R = 0.2239 (Rfree = 0.000) for 8175 atoms. Found 34 (55 requested) and removed 34 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 8417 seeds are put forward NCS extension: 14 residues added (14 deleted due to clashes), 8431 seeds are put forward Round 1: 713 peptides, 101 chains. Longest chain 22 peptides. Score 0.578 Round 2: 773 peptides, 83 chains. Longest chain 36 peptides. Score 0.704 Round 3: 778 peptides, 90 chains. Longest chain 26 peptides. Score 0.683 Round 4: 778 peptides, 86 chains. Longest chain 26 peptides. Score 0.697 Round 5: 768 peptides, 88 chains. Longest chain 28 peptides. Score 0.682 Taking the results from Round 2 Chains 86, Residues 690, Estimated correctness of the model 58.9 % 3 chains (60 residues) have been docked in sequence Building loops using Loopy2018 86 chains (690 residues) following loop building 3 chains (60 residues) in sequence following loop building ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 17391 restraints for refining 8262 atoms. 14452 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2506 (Rfree = 0.000) for 8262 atoms. Found 56 (56 requested) and removed 45 (31 requested) atoms. Cycle 17: After refmac, R = 0.2454 (Rfree = 0.000) for 8236 atoms. Found 48 (55 requested) and removed 38 (31 requested) atoms. Cycle 18: After refmac, R = 0.2368 (Rfree = 0.000) for 8226 atoms. Found 50 (53 requested) and removed 40 (31 requested) atoms. Cycle 19: After refmac, R = 0.2321 (Rfree = 0.000) for 8212 atoms. Found 44 (52 requested) and removed 37 (31 requested) atoms. Cycle 20: After refmac, R = 0.2265 (Rfree = 0.000) for 8205 atoms. Found 37 (51 requested) and removed 34 (31 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 8464 seeds are put forward NCS extension: 52 residues added (2 deleted due to clashes), 8516 seeds are put forward Round 1: 692 peptides, 98 chains. Longest chain 27 peptides. Score 0.570 Round 2: 771 peptides, 87 chains. Longest chain 27 peptides. Score 0.688 Round 3: 766 peptides, 96 chains. Longest chain 30 peptides. Score 0.650 Round 4: 765 peptides, 87 chains. Longest chain 31 peptides. Score 0.683 Round 5: 797 peptides, 87 chains. Longest chain 36 peptides. Score 0.709 Taking the results from Round 5 Chains 91, Residues 710, Estimated correctness of the model 60.2 % 2 chains (37 residues) have been docked in sequence Building loops using Loopy2018 91 chains (710 residues) following loop building 2 chains (37 residues) in sequence following loop building ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 17596 restraints for refining 8263 atoms. 14704 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2750 (Rfree = 0.000) for 8263 atoms. Found 50 (50 requested) and removed 52 (31 requested) atoms. Cycle 22: After refmac, R = 0.2523 (Rfree = 0.000) for 8211 atoms. Found 48 (48 requested) and removed 43 (31 requested) atoms. Cycle 23: After refmac, R = 0.2415 (Rfree = 0.000) for 8193 atoms. Found 47 (47 requested) and removed 39 (31 requested) atoms. Cycle 24: After refmac, R = 0.2317 (Rfree = 0.000) for 8177 atoms. Found 39 (45 requested) and removed 35 (30 requested) atoms. Cycle 25: After refmac, R = 0.2243 (Rfree = 0.000) for 8161 atoms. Found 40 (44 requested) and removed 38 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 8412 seeds are put forward NCS extension: 13 residues added (12 deleted due to clashes), 8425 seeds are put forward Round 1: 668 peptides, 99 chains. Longest chain 29 peptides. Score 0.539 Round 2: 747 peptides, 91 chains. Longest chain 36 peptides. Score 0.653 Round 3: 761 peptides, 90 chains. Longest chain 22 peptides. Score 0.669 Round 4: 728 peptides, 85 chains. Longest chain 35 peptides. Score 0.660 Round 5: 730 peptides, 84 chains. Longest chain 35 peptides. Score 0.666 Taking the results from Round 3 Chains 91, Residues 671, Estimated correctness of the model 49.6 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 18069 restraints for refining 8263 atoms. 15423 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2481 (Rfree = 0.000) for 8263 atoms. Found 43 (43 requested) and removed 37 (31 requested) atoms. Cycle 27: After refmac, R = 0.2355 (Rfree = 0.000) for 8243 atoms. Found 43 (43 requested) and removed 36 (31 requested) atoms. Cycle 28: After refmac, R = 0.2333 (Rfree = 0.000) for 8231 atoms. Found 43 (43 requested) and removed 37 (31 requested) atoms. Cycle 29: After refmac, R = 0.2280 (Rfree = 0.000) for 8215 atoms. Found 42 (43 requested) and removed 35 (31 requested) atoms. Cycle 30: After refmac, R = 0.2266 (Rfree = 0.000) for 8215 atoms. Found 43 (43 requested) and removed 40 (31 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 8490 seeds are put forward NCS extension: 18 residues added (7 deleted due to clashes), 8508 seeds are put forward Round 1: 647 peptides, 100 chains. Longest chain 20 peptides. Score 0.510 Round 2: 694 peptides, 89 chains. Longest chain 17 peptides. Score 0.612 Round 3: 709 peptides, 85 chains. Longest chain 30 peptides. Score 0.643 Round 4: 733 peptides, 87 chains. Longest chain 22 peptides. Score 0.656 Round 5: 705 peptides, 84 chains. Longest chain 23 peptides. Score 0.644 Taking the results from Round 4 Chains 88, Residues 646, Estimated correctness of the model 45.9 % 3 chains (42 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 17848 restraints for refining 8262 atoms. 15194 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2525 (Rfree = 0.000) for 8262 atoms. Found 43 (43 requested) and removed 41 (31 requested) atoms. Cycle 32: After refmac, R = 0.2409 (Rfree = 0.000) for 8233 atoms. Found 43 (43 requested) and removed 34 (31 requested) atoms. Cycle 33: After refmac, R = 0.2345 (Rfree = 0.000) for 8224 atoms. Found 43 (43 requested) and removed 33 (31 requested) atoms. Cycle 34: After refmac, R = 0.2261 (Rfree = 0.000) for 8220 atoms. Found 36 (43 requested) and removed 36 (31 requested) atoms. Cycle 35: After refmac, R = 0.2200 (Rfree = 0.000) for 8206 atoms. Found 41 (43 requested) and removed 35 (31 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 8453 seeds are put forward NCS extension: 13 residues added (12 deleted due to clashes), 8466 seeds are put forward Round 1: 629 peptides, 98 chains. Longest chain 20 peptides. Score 0.500 Round 2: 672 peptides, 86 chains. Longest chain 26 peptides. Score 0.604 Round 3: 681 peptides, 87 chains. Longest chain 24 peptides. Score 0.608 Round 4: 670 peptides, 84 chains. Longest chain 30 peptides. Score 0.610 Round 5: 681 peptides, 89 chains. Longest chain 23 peptides. Score 0.599 Taking the results from Round 4 Chains 85, Residues 586, Estimated correctness of the model 31.9 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 18480 restraints for refining 8263 atoms. 16186 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2462 (Rfree = 0.000) for 8263 atoms. Found 43 (43 requested) and removed 41 (31 requested) atoms. Cycle 37: After refmac, R = 0.2381 (Rfree = 0.000) for 8236 atoms. Found 43 (43 requested) and removed 32 (31 requested) atoms. Cycle 38: After refmac, R = 0.2123 (Rfree = 0.000) for 8222 atoms. Found 23 (43 requested) and removed 32 (31 requested) atoms. Cycle 39: After refmac, R = 0.2175 (Rfree = 0.000) for 8202 atoms. Found 34 (43 requested) and removed 36 (31 requested) atoms. Cycle 40: After refmac, R = 0.2055 (Rfree = 0.000) for 8187 atoms. Found 20 (43 requested) and removed 33 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.19 3.28 Search for helices and strands: 0 residues in 0 chains, 8394 seeds are put forward NCS extension: 18 residues added (14 deleted due to clashes), 8412 seeds are put forward Round 1: 591 peptides, 93 chains. Longest chain 21 peptides. Score 0.480 Round 2: 646 peptides, 91 chains. Longest chain 18 peptides. Score 0.553 Round 3: 652 peptides, 86 chains. Longest chain 22 peptides. Score 0.583 Round 4: 667 peptides, 86 chains. Longest chain 19 peptides. Score 0.599 Round 5: 664 peptides, 83 chains. Longest chain 22 peptides. Score 0.609 Taking the results from Round 5 Chains 85, Residues 581, Estimated correctness of the model 31.6 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 16942 reflections ( 99.75 % complete ) and 18162 restraints for refining 8261 atoms. 15833 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2458 (Rfree = 0.000) for 8261 atoms. Found 43 (43 requested) and removed 38 (31 requested) atoms. Cycle 42: After refmac, R = 0.2431 (Rfree = 0.000) for 8231 atoms. Found 43 (43 requested) and removed 42 (31 requested) atoms. Cycle 43: After refmac, R = 0.2319 (Rfree = 0.000) for 8219 atoms. Found 43 (43 requested) and removed 34 (31 requested) atoms. Cycle 44: After refmac, R = 0.2272 (Rfree = 0.000) for 8212 atoms. Found 43 (43 requested) and removed 36 (31 requested) atoms. Cycle 45: After refmac, R = 0.2262 (Rfree = 0.000) for 8207 atoms. Found 43 (43 requested) and removed 35 (31 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 8433 seeds are put forward NCS extension: 9 residues added (5 deleted due to clashes), 8442 seeds are put forward Round 1: 525 peptides, 92 chains. Longest chain 15 peptides. Score 0.401 Round 2: 608 peptides, 87 chains. Longest chain 23 peptides. Score 0.531 Round 3: 606 peptides, 87 chains. Longest chain 16 peptides. Score 0.529 Round 4: 645 peptides, 97 chains. Longest chain 16 peptides. Score 0.523 Round 5: 636 peptides, 93 chains. Longest chain 17 peptides. Score 0.533 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 93, Residues 543, Estimated correctness of the model 5.3 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2hx1-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16942 reflections ( 99.75 % complete ) and 18937 restraints for refining 8263 atoms. 16858 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2416 (Rfree = 0.000) for 8263 atoms. Found 0 (43 requested) and removed 31 (31 requested) atoms. Cycle 47: After refmac, R = 0.2393 (Rfree = 0.000) for 8214 atoms. Found 0 (43 requested) and removed 31 (31 requested) atoms. Cycle 48: After refmac, R = 0.2360 (Rfree = 0.000) for 8169 atoms. Found 0 (43 requested) and removed 30 (30 requested) atoms. Cycle 49: After refmac, R = 0.2336 (Rfree = 0.000) for 8134 atoms. Found 0 (43 requested) and removed 30 (30 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 02:31:25 GMT 2018 Job finished. TimeTaking 98.3 Used memory is bytes: 16629848