Mon 24 Dec 07:36:53 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2hx1-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2hx1-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2hx1-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.6-parrot-noncs ############### 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 07:36:58 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/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.6-parrot-noncs/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 849 and 0 Target number of residues in the AU: 849 Target solvent content: 0.6126 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: 2hx1-3.6-parrot-noncs.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: 2hx1-3.6-parrot-noncs.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 3.600 Wilson plot Bfac: 58.00 14332 reflections ( 99.70 % complete ) and 0 restraints for refining 10023 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3373 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3202 (Rfree = 0.000) for 10023 atoms. Found 64 (64 requested) and removed 61 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 3.34 Search for helices and strands: 0 residues in 0 chains, 10212 seeds are put forward NCS extension: 0 residues added, 10212 seeds are put forward Round 1: 483 peptides, 97 chains. Longest chain 10 peptides. Score 0.313 Round 2: 623 peptides, 104 chains. Longest chain 31 peptides. Score 0.461 Round 3: 660 peptides, 104 chains. Longest chain 20 peptides. Score 0.505 Round 4: 675 peptides, 101 chains. Longest chain 28 peptides. Score 0.537 Round 5: 695 peptides, 96 chains. Longest chain 34 peptides. Score 0.582 Taking the results from Round 5 Chains 97, Residues 599, Estimated correctness of the model 7.5 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 18421 restraints for refining 8236 atoms. 16105 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2893 (Rfree = 0.000) for 8236 atoms. Found 52 (52 requested) and removed 121 (26 requested) atoms. Cycle 2: After refmac, R = 0.2676 (Rfree = 0.000) for 8048 atoms. Found 52 (52 requested) and removed 40 (26 requested) atoms. Cycle 3: After refmac, R = 0.2492 (Rfree = 0.000) for 7974 atoms. Found 51 (51 requested) and removed 40 (25 requested) atoms. Cycle 4: After refmac, R = 0.2243 (Rfree = 0.000) for 7932 atoms. Found 24 (51 requested) and removed 30 (25 requested) atoms. Cycle 5: After refmac, R = 0.2172 (Rfree = 0.000) for 7899 atoms. Found 24 (50 requested) and removed 34 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 8167 seeds are put forward NCS extension: 45 residues added (14 deleted due to clashes), 8212 seeds are put forward Round 1: 570 peptides, 102 chains. Longest chain 19 peptides. Score 0.404 Round 2: 666 peptides, 97 chains. Longest chain 27 peptides. Score 0.546 Round 3: 669 peptides, 99 chains. Longest chain 23 peptides. Score 0.540 Round 4: 663 peptides, 94 chains. Longest chain 22 peptides. Score 0.557 Round 5: 663 peptides, 86 chains. Longest chain 35 peptides. Score 0.595 Taking the results from Round 5 Chains 87, Residues 577, Estimated correctness of the model 12.7 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 18574 restraints for refining 8229 atoms. 16317 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2696 (Rfree = 0.000) for 8229 atoms. Found 52 (52 requested) and removed 69 (26 requested) atoms. Cycle 7: After refmac, R = 0.2655 (Rfree = 0.000) for 8153 atoms. Found 52 (52 requested) and removed 52 (26 requested) atoms. Cycle 8: After refmac, R = 0.2516 (Rfree = 0.000) for 8110 atoms. Found 52 (52 requested) and removed 51 (26 requested) atoms. Cycle 9: After refmac, R = 0.2433 (Rfree = 0.000) for 8088 atoms. Found 48 (52 requested) and removed 47 (26 requested) atoms. Cycle 10: After refmac, R = 0.2335 (Rfree = 0.000) for 8074 atoms. Found 43 (51 requested) and removed 43 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.42 Search for helices and strands: 0 residues in 0 chains, 8344 seeds are put forward NCS extension: 18 residues added (22 deleted due to clashes), 8362 seeds are put forward Round 1: 607 peptides, 102 chains. Longest chain 22 peptides. Score 0.452 Round 2: 665 peptides, 90 chains. Longest chain 27 peptides. Score 0.578 Round 3: 632 peptides, 86 chains. Longest chain 25 peptides. Score 0.562 Round 4: 653 peptides, 82 chains. Longest chain 19 peptides. Score 0.603 Round 5: 653 peptides, 82 chains. Longest chain 34 peptides. Score 0.603 Taking the results from Round 5 Chains 83, Residues 571, Estimated correctness of the model 15.8 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 18588 restraints for refining 8237 atoms. 16358 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2772 (Rfree = 0.000) for 8237 atoms. Found 52 (52 requested) and removed 38 (26 requested) atoms. Cycle 12: After refmac, R = 0.2466 (Rfree = 0.000) for 8210 atoms. Found 52 (52 requested) and removed 50 (26 requested) atoms. Cycle 13: After refmac, R = 0.2335 (Rfree = 0.000) for 8196 atoms. Found 37 (52 requested) and removed 46 (26 requested) atoms. Cycle 14: After refmac, R = 0.2285 (Rfree = 0.000) for 8170 atoms. Found 38 (52 requested) and removed 46 (26 requested) atoms. Cycle 15: After refmac, R = 0.2236 (Rfree = 0.000) for 8156 atoms. Found 46 (52 requested) and removed 40 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.35 Search for helices and strands: 0 residues in 0 chains, 8403 seeds are put forward NCS extension: 32 residues added (19 deleted due to clashes), 8435 seeds are put forward Round 1: 543 peptides, 94 chains. Longest chain 16 peptides. Score 0.414 Round 2: 635 peptides, 93 chains. Longest chain 20 peptides. Score 0.531 Round 3: 619 peptides, 87 chains. Longest chain 26 peptides. Score 0.543 Round 4: 634 peptides, 90 chains. Longest chain 18 peptides. Score 0.545 Round 5: 632 peptides, 86 chains. Longest chain 19 peptides. Score 0.562 Taking the results from Round 5 Chains 88, Residues 546, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 18499 restraints for refining 8238 atoms. 16330 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2607 (Rfree = 0.000) for 8238 atoms. Found 52 (52 requested) and removed 46 (26 requested) atoms. Cycle 17: After refmac, R = 0.2325 (Rfree = 0.000) for 8178 atoms. Found 38 (52 requested) and removed 43 (26 requested) atoms. Cycle 18: After refmac, R = 0.2184 (Rfree = 0.000) for 8141 atoms. Found 26 (52 requested) and removed 33 (26 requested) atoms. Cycle 19: After refmac, R = 0.2081 (Rfree = 0.000) for 8122 atoms. Found 20 (52 requested) and removed 31 (26 requested) atoms. Cycle 20: After refmac, R = 0.2069 (Rfree = 0.000) for 8091 atoms. Found 26 (52 requested) and removed 33 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 8325 seeds are put forward NCS extension: 9 residues added (7 deleted due to clashes), 8334 seeds are put forward Round 1: 522 peptides, 95 chains. Longest chain 16 peptides. Score 0.380 Round 2: 594 peptides, 89 chains. Longest chain 22 peptides. Score 0.505 Round 3: 585 peptides, 86 chains. Longest chain 16 peptides. Score 0.509 Round 4: 595 peptides, 84 chains. Longest chain 18 peptides. Score 0.531 Round 5: 581 peptides, 81 chains. Longest chain 22 peptides. Score 0.530 Taking the results from Round 4 Chains 84, Residues 511, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 18870 restraints for refining 8237 atoms. 16910 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2526 (Rfree = 0.000) for 8237 atoms. Found 52 (52 requested) and removed 48 (26 requested) atoms. Cycle 22: After refmac, R = 0.2258 (Rfree = 0.000) for 8188 atoms. Found 38 (52 requested) and removed 36 (26 requested) atoms. Cycle 23: After refmac, R = 0.2138 (Rfree = 0.000) for 8173 atoms. Found 31 (52 requested) and removed 41 (26 requested) atoms. Cycle 24: After refmac, R = 0.2076 (Rfree = 0.000) for 8146 atoms. Found 34 (52 requested) and removed 40 (26 requested) atoms. Cycle 25: After refmac, R = 0.2061 (Rfree = 0.000) for 8129 atoms. Found 31 (52 requested) and removed 41 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 8332 seeds are put forward NCS extension: 10 residues added (4 deleted due to clashes), 8342 seeds are put forward Round 1: 506 peptides, 95 chains. Longest chain 13 peptides. Score 0.358 Round 2: 592 peptides, 97 chains. Longest chain 14 peptides. Score 0.460 Round 3: 587 peptides, 92 chains. Longest chain 15 peptides. Score 0.480 Round 4: 582 peptides, 87 chains. Longest chain 18 peptides. Score 0.501 Round 5: 606 peptides, 87 chains. Longest chain 17 peptides. Score 0.529 Taking the results from Round 5 Chains 88, Residues 519, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 18800 restraints for refining 8237 atoms. 16795 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2456 (Rfree = 0.000) for 8237 atoms. Found 52 (52 requested) and removed 38 (26 requested) atoms. Cycle 27: After refmac, R = 0.2438 (Rfree = 0.000) for 8215 atoms. Found 52 (52 requested) and removed 33 (26 requested) atoms. Cycle 28: After refmac, R = 0.2255 (Rfree = 0.000) for 8218 atoms. Found 52 (52 requested) and removed 42 (26 requested) atoms. Cycle 29: After refmac, R = 0.2125 (Rfree = 0.000) for 8218 atoms. Found 52 (52 requested) and removed 35 (26 requested) atoms. Cycle 30: After refmac, R = 0.2017 (Rfree = 0.000) for 8223 atoms. Found 42 (52 requested) and removed 37 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 8479 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 8496 seeds are put forward Round 1: 491 peptides, 96 chains. Longest chain 13 peptides. Score 0.331 Round 2: 549 peptides, 86 chains. Longest chain 22 peptides. Score 0.466 Round 3: 565 peptides, 90 chains. Longest chain 24 peptides. Score 0.464 Round 4: 555 peptides, 83 chains. Longest chain 16 peptides. Score 0.489 Round 5: 551 peptides, 86 chains. Longest chain 16 peptides. Score 0.468 Taking the results from Round 4 Chains 85, Residues 472, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 18926 restraints for refining 8238 atoms. 17033 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2275 (Rfree = 0.000) for 8238 atoms. Found 35 (52 requested) and removed 37 (26 requested) atoms. Cycle 32: After refmac, R = 0.2090 (Rfree = 0.000) for 8192 atoms. Found 40 (52 requested) and removed 38 (26 requested) atoms. Cycle 33: After refmac, R = 0.2046 (Rfree = 0.000) for 8179 atoms. Found 34 (52 requested) and removed 39 (26 requested) atoms. Cycle 34: After refmac, R = 0.1959 (Rfree = 0.000) for 8167 atoms. Found 41 (52 requested) and removed 31 (26 requested) atoms. Cycle 35: After refmac, R = 0.1923 (Rfree = 0.000) for 8168 atoms. Found 38 (52 requested) and removed 33 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.25 3.34 Search for helices and strands: 0 residues in 0 chains, 8392 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 8406 seeds are put forward Round 1: 454 peptides, 83 chains. Longest chain 13 peptides. Score 0.357 Round 2: 521 peptides, 83 chains. Longest chain 26 peptides. Score 0.447 Round 3: 504 peptides, 78 chains. Longest chain 20 peptides. Score 0.453 Round 4: 504 peptides, 74 chains. Longest chain 20 peptides. Score 0.476 Round 5: 509 peptides, 76 chains. Longest chain 26 peptides. Score 0.471 Taking the results from Round 4 Chains 76, Residues 430, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 19210 restraints for refining 8238 atoms. 17520 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2173 (Rfree = 0.000) for 8238 atoms. Found 52 (52 requested) and removed 38 (26 requested) atoms. Cycle 37: After refmac, R = 0.1943 (Rfree = 0.000) for 8235 atoms. Found 21 (52 requested) and removed 32 (26 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1944 (Rfree = 0.000) for 8216 atoms. Found 23 (52 requested) and removed 28 (26 requested) atoms. Cycle 39: After refmac, R = 0.1924 (Rfree = 0.000) for 8200 atoms. Found 25 (52 requested) and removed 32 (26 requested) atoms. Cycle 40: After refmac, R = 0.1843 (Rfree = 0.000) for 8185 atoms. Found 30 (52 requested) and removed 34 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.34 Search for helices and strands: 0 residues in 0 chains, 8379 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 8404 seeds are put forward Round 1: 428 peptides, 85 chains. Longest chain 14 peptides. Score 0.306 Round 2: 526 peptides, 89 chains. Longest chain 21 peptides. Score 0.420 Round 3: 527 peptides, 86 chains. Longest chain 16 peptides. Score 0.438 Round 4: 520 peptides, 82 chains. Longest chain 14 peptides. Score 0.451 Round 5: 523 peptides, 79 chains. Longest chain 15 peptides. Score 0.472 Taking the results from Round 5 Chains 81, Residues 444, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 18974 restraints for refining 8237 atoms. 17251 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2205 (Rfree = 0.000) for 8237 atoms. Found 51 (52 requested) and removed 36 (26 requested) atoms. Cycle 42: After refmac, R = 0.1959 (Rfree = 0.000) for 8217 atoms. Found 28 (52 requested) and removed 32 (26 requested) atoms. Cycle 43: After refmac, R = 0.1884 (Rfree = 0.000) for 8192 atoms. Found 30 (52 requested) and removed 29 (26 requested) atoms. Cycle 44: After refmac, R = 0.1810 (Rfree = 0.000) for 8177 atoms. Found 33 (52 requested) and removed 32 (26 requested) atoms. Cycle 45: After refmac, R = 0.1783 (Rfree = 0.000) for 8171 atoms. Found 48 (52 requested) and removed 29 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 3.32 Search for helices and strands: 0 residues in 0 chains, 8416 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 8432 seeds are put forward Round 1: 422 peptides, 81 chains. Longest chain 12 peptides. Score 0.323 Round 2: 488 peptides, 77 chains. Longest chain 19 peptides. Score 0.438 Round 3: 494 peptides, 77 chains. Longest chain 16 peptides. Score 0.446 Round 4: 509 peptides, 77 chains. Longest chain 18 peptides. Score 0.465 Round 5: 512 peptides, 73 chains. Longest chain 19 peptides. Score 0.491 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 75, Residues 439, Estimated correctness of the model 0.0 % 3 chains (33 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2hx1-3_warpNtrace.pdb as input Building loops using Loopy2018 75 chains (439 residues) following loop building 3 chains (33 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14332 reflections ( 99.70 % complete ) and 18641 restraints for refining 8238 atoms. 16816 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2151 (Rfree = 0.000) for 8238 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 47: After refmac, R = 0.2025 (Rfree = 0.000) for 8187 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 48: After refmac, R = 0.2026 (Rfree = 0.000) for 8142 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 49: After refmac, R = 0.1936 (Rfree = 0.000) for 8107 atoms. TimeTaking 87.17