null Sun 23 Dec 22:22:52 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 2it9-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2it9-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2it9-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2it9-3.2-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/2it9-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2it9-3.2-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 22:23:02 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/2it9-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2it9-3.2-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 418 and 0 Target number of residues in the AU: 418 Target solvent content: 0.6240 Checking the provided sequence file Detected sequence length: 127 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 508 Adjusted target solvent content: 0.54 Input MTZ file: 2it9-3.2-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: 19 Cell parameters: 59.723 81.014 124.347 90.000 90.000 90.000 Input sequence file: 2it9-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 4064 target number of atoms Had to go as low as 0.80 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: 67.879 3.200 Wilson plot Bfac: 63.35 10303 reflections ( 98.61 % complete ) and 0 restraints for refining 4542 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3678 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2908 (Rfree = 0.000) for 4542 atoms. Found 39 (40 requested) and removed 45 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.17 3.01 Search for helices and strands: 0 residues in 0 chains, 4606 seeds are put forward NCS extension: 0 residues added, 4606 seeds are put forward Round 1: 247 peptides, 46 chains. Longest chain 14 peptides. Score 0.357 Round 2: 299 peptides, 46 chains. Longest chain 18 peptides. Score 0.490 Round 3: 311 peptides, 44 chains. Longest chain 23 peptides. Score 0.538 Round 4: 301 peptides, 41 chains. Longest chain 18 peptides. Score 0.545 Round 5: 308 peptides, 40 chains. Longest chain 20 peptides. Score 0.570 Taking the results from Round 5 Chains 40, Residues 268, Estimated correctness of the model 32.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 8026 restraints for refining 3706 atoms. 6994 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2597 (Rfree = 0.000) for 3706 atoms. Found 33 (33 requested) and removed 22 (16 requested) atoms. Cycle 2: After refmac, R = 0.2582 (Rfree = 0.000) for 3683 atoms. Found 18 (33 requested) and removed 21 (16 requested) atoms. Cycle 3: After refmac, R = 0.2519 (Rfree = 0.000) for 3661 atoms. Found 20 (33 requested) and removed 23 (16 requested) atoms. Cycle 4: After refmac, R = 0.2220 (Rfree = 0.000) for 3638 atoms. Found 12 (32 requested) and removed 18 (16 requested) atoms. Cycle 5: After refmac, R = 0.2154 (Rfree = 0.000) for 3623 atoms. Found 6 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 3740 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3763 seeds are put forward Round 1: 288 peptides, 49 chains. Longest chain 15 peptides. Score 0.431 Round 2: 313 peptides, 45 chains. Longest chain 20 peptides. Score 0.532 Round 3: 308 peptides, 40 chains. Longest chain 18 peptides. Score 0.570 Round 4: 324 peptides, 43 chains. Longest chain 21 peptides. Score 0.575 Round 5: 328 peptides, 42 chains. Longest chain 17 peptides. Score 0.592 Taking the results from Round 5 Chains 42, Residues 286, Estimated correctness of the model 38.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 7869 restraints for refining 3708 atoms. 6767 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2514 (Rfree = 0.000) for 3708 atoms. Found 28 (33 requested) and removed 22 (16 requested) atoms. Cycle 7: After refmac, R = 0.2387 (Rfree = 0.000) for 3687 atoms. Found 19 (33 requested) and removed 19 (16 requested) atoms. Cycle 8: After refmac, R = 0.2436 (Rfree = 0.000) for 3672 atoms. Found 28 (33 requested) and removed 20 (16 requested) atoms. Cycle 9: After refmac, R = 0.2281 (Rfree = 0.000) for 3672 atoms. Found 12 (33 requested) and removed 19 (16 requested) atoms. Cycle 10: After refmac, R = 0.2241 (Rfree = 0.000) for 3657 atoms. Found 19 (32 requested) and removed 25 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 2.96 Search for helices and strands: 0 residues in 0 chains, 3804 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 3822 seeds are put forward Round 1: 270 peptides, 45 chains. Longest chain 15 peptides. Score 0.429 Round 2: 311 peptides, 42 chains. Longest chain 19 peptides. Score 0.557 Round 3: 323 peptides, 41 chains. Longest chain 17 peptides. Score 0.591 Round 4: 323 peptides, 43 chains. Longest chain 18 peptides. Score 0.573 Round 5: 316 peptides, 42 chains. Longest chain 20 peptides. Score 0.568 Taking the results from Round 3 Chains 41, Residues 282, Estimated correctness of the model 38.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 7904 restraints for refining 3710 atoms. 6817 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2464 (Rfree = 0.000) for 3710 atoms. Found 22 (33 requested) and removed 23 (16 requested) atoms. Cycle 12: After refmac, R = 0.2439 (Rfree = 0.000) for 3699 atoms. Found 20 (33 requested) and removed 19 (16 requested) atoms. Cycle 13: After refmac, R = 0.2453 (Rfree = 0.000) for 3687 atoms. Found 30 (33 requested) and removed 18 (16 requested) atoms. Cycle 14: After refmac, R = 0.2348 (Rfree = 0.000) for 3690 atoms. Found 20 (33 requested) and removed 18 (16 requested) atoms. Cycle 15: After refmac, R = 0.2383 (Rfree = 0.000) for 3688 atoms. Found 32 (33 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 3836 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 3853 seeds are put forward Round 1: 278 peptides, 45 chains. Longest chain 19 peptides. Score 0.450 Round 2: 327 peptides, 44 chains. Longest chain 18 peptides. Score 0.572 Round 3: 322 peptides, 45 chains. Longest chain 19 peptides. Score 0.552 Round 4: 301 peptides, 40 chains. Longest chain 20 peptides. Score 0.555 Round 5: 304 peptides, 43 chains. Longest chain 21 peptides. Score 0.532 Taking the results from Round 2 Chains 44, Residues 283, Estimated correctness of the model 33.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 7889 restraints for refining 3710 atoms. 6801 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2515 (Rfree = 0.000) for 3710 atoms. Found 28 (33 requested) and removed 19 (16 requested) atoms. Cycle 17: After refmac, R = 0.2440 (Rfree = 0.000) for 3702 atoms. Found 16 (33 requested) and removed 18 (16 requested) atoms. Cycle 18: After refmac, R = 0.2490 (Rfree = 0.000) for 3688 atoms. Found 23 (33 requested) and removed 20 (16 requested) atoms. Cycle 19: After refmac, R = 0.2501 (Rfree = 0.000) for 3679 atoms. Found 29 (33 requested) and removed 16 (16 requested) atoms. Cycle 20: After refmac, R = 0.2335 (Rfree = 0.000) for 3679 atoms. Found 19 (33 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 3.00 Search for helices and strands: 0 residues in 0 chains, 3784 seeds are put forward NCS extension: 14 residues added (5 deleted due to clashes), 3798 seeds are put forward Round 1: 274 peptides, 48 chains. Longest chain 16 peptides. Score 0.406 Round 2: 307 peptides, 44 chains. Longest chain 16 peptides. Score 0.529 Round 3: 313 peptides, 44 chains. Longest chain 18 peptides. Score 0.542 Round 4: 304 peptides, 43 chains. Longest chain 15 peptides. Score 0.532 Round 5: 313 peptides, 39 chains. Longest chain 20 peptides. Score 0.589 Taking the results from Round 5 Chains 39, Residues 274, Estimated correctness of the model 38.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 7936 restraints for refining 3710 atoms. 6879 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2648 (Rfree = 0.000) for 3710 atoms. Found 33 (33 requested) and removed 18 (16 requested) atoms. Cycle 22: After refmac, R = 0.2369 (Rfree = 0.000) for 3714 atoms. Found 18 (33 requested) and removed 20 (16 requested) atoms. Cycle 23: After refmac, R = 0.2343 (Rfree = 0.000) for 3701 atoms. Found 15 (33 requested) and removed 16 (16 requested) atoms. Cycle 24: After refmac, R = 0.2327 (Rfree = 0.000) for 3696 atoms. Found 18 (33 requested) and removed 18 (16 requested) atoms. Cycle 25: After refmac, R = 0.2340 (Rfree = 0.000) for 3693 atoms. Found 30 (33 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.11 2.95 Search for helices and strands: 0 residues in 0 chains, 3839 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 3861 seeds are put forward Round 1: 280 peptides, 44 chains. Longest chain 15 peptides. Score 0.465 Round 2: 304 peptides, 41 chains. Longest chain 21 peptides. Score 0.551 Round 3: 327 peptides, 46 chains. Longest chain 22 peptides. Score 0.553 Round 4: 321 peptides, 43 chains. Longest chain 20 peptides. Score 0.569 Round 5: 324 peptides, 39 chains. Longest chain 20 peptides. Score 0.611 Taking the results from Round 5 Chains 39, Residues 285, Estimated correctness of the model 44.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 7722 restraints for refining 3709 atoms. 6598 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2448 (Rfree = 0.000) for 3709 atoms. Found 23 (33 requested) and removed 21 (16 requested) atoms. Cycle 27: After refmac, R = 0.2345 (Rfree = 0.000) for 3701 atoms. Found 9 (33 requested) and removed 17 (16 requested) atoms. Cycle 28: After refmac, R = 0.2243 (Rfree = 0.000) for 3688 atoms. Found 9 (33 requested) and removed 17 (16 requested) atoms. Cycle 29: After refmac, R = 0.2249 (Rfree = 0.000) for 3671 atoms. Found 14 (33 requested) and removed 19 (16 requested) atoms. Cycle 30: After refmac, R = 0.2152 (Rfree = 0.000) for 3662 atoms. Found 7 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.19 3.02 Search for helices and strands: 0 residues in 0 chains, 3743 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 3764 seeds are put forward Round 1: 268 peptides, 47 chains. Longest chain 13 peptides. Score 0.402 Round 2: 310 peptides, 44 chains. Longest chain 16 peptides. Score 0.535 Round 3: 297 peptides, 40 chains. Longest chain 16 peptides. Score 0.546 Round 4: 297 peptides, 41 chains. Longest chain 23 peptides. Score 0.536 Round 5: 310 peptides, 39 chains. Longest chain 21 peptides. Score 0.583 Taking the results from Round 5 Chains 41, Residues 271, Estimated correctness of the model 36.4 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 7739 restraints for refining 3710 atoms. 6650 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2443 (Rfree = 0.000) for 3710 atoms. Found 17 (33 requested) and removed 17 (16 requested) atoms. Cycle 32: After refmac, R = 0.2285 (Rfree = 0.000) for 3699 atoms. Found 7 (33 requested) and removed 17 (16 requested) atoms. Cycle 33: After refmac, R = 0.2327 (Rfree = 0.000) for 3684 atoms. Found 10 (33 requested) and removed 17 (16 requested) atoms. Cycle 34: After refmac, R = 0.2250 (Rfree = 0.000) for 3673 atoms. Found 5 (32 requested) and removed 17 (16 requested) atoms. Cycle 35: After refmac, R = 0.2176 (Rfree = 0.000) for 3657 atoms. Found 7 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 3.00 Search for helices and strands: 0 residues in 0 chains, 3743 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 3770 seeds are put forward Round 1: 242 peptides, 40 chains. Longest chain 12 peptides. Score 0.413 Round 2: 276 peptides, 39 chains. Longest chain 20 peptides. Score 0.509 Round 3: 277 peptides, 37 chains. Longest chain 19 peptides. Score 0.531 Round 4: 288 peptides, 35 chains. Longest chain 18 peptides. Score 0.575 Round 5: 294 peptides, 36 chains. Longest chain 21 peptides. Score 0.578 Taking the results from Round 5 Chains 36, Residues 258, Estimated correctness of the model 35.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 7917 restraints for refining 3710 atoms. 6921 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2328 (Rfree = 0.000) for 3710 atoms. Found 22 (33 requested) and removed 18 (16 requested) atoms. Cycle 37: After refmac, R = 0.2280 (Rfree = 0.000) for 3707 atoms. Found 13 (33 requested) and removed 17 (16 requested) atoms. Cycle 38: After refmac, R = 0.2149 (Rfree = 0.000) for 3695 atoms. Found 10 (33 requested) and removed 17 (16 requested) atoms. Cycle 39: After refmac, R = 0.2052 (Rfree = 0.000) for 3687 atoms. Found 5 (33 requested) and removed 16 (16 requested) atoms. Cycle 40: After refmac, R = 0.2077 (Rfree = 0.000) for 3675 atoms. Found 8 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 3776 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 3803 seeds are put forward Round 1: 263 peptides, 41 chains. Longest chain 17 peptides. Score 0.456 Round 2: 285 peptides, 36 chains. Longest chain 24 peptides. Score 0.559 Round 3: 282 peptides, 38 chains. Longest chain 19 peptides. Score 0.533 Round 4: 275 peptides, 36 chains. Longest chain 23 peptides. Score 0.537 Round 5: 262 peptides, 35 chains. Longest chain 15 peptides. Score 0.518 Taking the results from Round 2 Chains 36, Residues 249, Estimated correctness of the model 29.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10303 reflections ( 98.61 % complete ) and 7840 restraints for refining 3710 atoms. 6880 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2168 (Rfree = 0.000) for 3710 atoms. Found 13 (33 requested) and removed 16 (16 requested) atoms. Cycle 42: After refmac, R = 0.2105 (Rfree = 0.000) for 3700 atoms. Found 6 (33 requested) and removed 17 (16 requested) atoms. Cycle 43: After refmac, R = 0.2151 (Rfree = 0.000) for 3688 atoms. Found 11 (33 requested) and removed 16 (16 requested) atoms. Cycle 44: After refmac, R = 0.2059 (Rfree = 0.000) for 3678 atoms. Found 11 (33 requested) and removed 17 (16 requested) atoms. Cycle 45: After refmac, R = 0.2041 (Rfree = 0.000) for 3670 atoms. Found 8 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 3747 seeds are put forward NCS extension: 34 residues added (6 deleted due to clashes), 3781 seeds are put forward Round 1: 243 peptides, 40 chains. Longest chain 12 peptides. Score 0.416 Round 2: 262 peptides, 40 chains. Longest chain 24 peptides. Score 0.464 Round 3: 268 peptides, 36 chains. Longest chain 17 peptides. Score 0.521 Round 4: 282 peptides, 39 chains. Longest chain 25 peptides. Score 0.522 Round 5: 260 peptides, 34 chains. Longest chain 16 peptides. Score 0.523 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 226, Estimated correctness of the model 18.7 % 2 chains (17 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2it9-3_warpNtrace.pdb as input Building loops using Loopy2018 35 chains (226 residues) following loop building 2 chains (17 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10303 reflections ( 98.61 % complete ) and 7761 restraints for refining 3710 atoms. 6815 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2294 (Rfree = 0.000) for 3710 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2198 (Rfree = 0.000) for 3688 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2116 (Rfree = 0.000) for 3669 atoms. Found 0 (32 requested) and removed 12 (16 requested) atoms. Cycle 49: After refmac, R = 0.2124 (Rfree = 0.000) for 3657 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:21:00 GMT 2018 Job finished. TimeTaking 58.13 Used memory is bytes: 7734808