Mon 24 Dec 07:28:47 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 2gfg-2.1-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2gfg-2.1-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2gfg-2.1-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2gfg-2.1-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/2gfg-2.1-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2gfg-2.1-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 07:28:51 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/2gfg-2.1-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2gfg-2.1-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 513 and 0 Target number of residues in the AU: 513 Target solvent content: 0.5408 Checking the provided sequence file Detected sequence length: 193 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 579 Adjusted target solvent content: 0.48 Input MTZ file: 2gfg-2.1-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: 43.030 74.690 188.130 90.000 90.000 90.000 Input sequence file: 2gfg-2.1-parrot-noncs.fasta_lf Building free atoms model in initial map for 4632 target number of atoms Had to go as low as 0.55 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 1 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: 94.065 2.120 Wilson plot Bfac: 32.97 34827 reflections ( 98.30 % complete ) and 0 restraints for refining 5164 atoms. Observations/parameters ratio is 1.69 ------------------------------------------------------ Starting model: R = 0.3941 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3408 (Rfree = 0.000) for 5164 atoms. Found 83 (149 requested) and removed 101 (74 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.36 2.42 NCS extension: 0 residues added, 5146 seeds are put forward Round 1: 235 peptides, 50 chains. Longest chain 9 peptides. Score 0.274 Round 2: 276 peptides, 51 chains. Longest chain 10 peptides. Score 0.377 Round 3: 298 peptides, 54 chains. Longest chain 14 peptides. Score 0.402 Round 4: 304 peptides, 54 chains. Longest chain 15 peptides. Score 0.417 Round 5: 306 peptides, 54 chains. Longest chain 17 peptides. Score 0.422 Taking the results from Round 5 Chains 54, Residues 252, Estimated correctness of the model 68.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9562 restraints for refining 4447 atoms. 8608 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3683 (Rfree = 0.000) for 4447 atoms. Found 83 (129 requested) and removed 65 (64 requested) atoms. Cycle 2: After refmac, R = 0.3462 (Rfree = 0.000) for 4443 atoms. Found 56 (129 requested) and removed 65 (64 requested) atoms. Cycle 3: After refmac, R = 0.3306 (Rfree = 0.000) for 4422 atoms. Found 56 (128 requested) and removed 64 (64 requested) atoms. Cycle 4: After refmac, R = 0.3183 (Rfree = 0.000) for 4401 atoms. Found 48 (128 requested) and removed 56 (64 requested) atoms. Cycle 5: After refmac, R = 0.3093 (Rfree = 0.000) for 4388 atoms. Found 30 (127 requested) and removed 33 (63 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.32 2.38 NCS extension: 20 residues added (0 deleted due to clashes), 4471 seeds are put forward Round 1: 269 peptides, 52 chains. Longest chain 15 peptides. Score 0.347 Round 2: 298 peptides, 50 chains. Longest chain 13 peptides. Score 0.445 Round 3: 304 peptides, 48 chains. Longest chain 16 peptides. Score 0.481 Round 4: 310 peptides, 47 chains. Longest chain 15 peptides. Score 0.505 Round 5: 308 peptides, 46 chains. Longest chain 21 peptides. Score 0.510 Taking the results from Round 5 Chains 46, Residues 262, Estimated correctness of the model 76.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9786 restraints for refining 4448 atoms. 8784 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3399 (Rfree = 0.000) for 4448 atoms. Found 83 (129 requested) and removed 64 (64 requested) atoms. Cycle 7: After refmac, R = 0.3206 (Rfree = 0.000) for 4463 atoms. Found 62 (129 requested) and removed 64 (64 requested) atoms. Cycle 8: After refmac, R = 0.3121 (Rfree = 0.000) for 4461 atoms. Found 39 (129 requested) and removed 38 (64 requested) atoms. Cycle 9: After refmac, R = 0.3037 (Rfree = 0.000) for 4457 atoms. Found 34 (129 requested) and removed 33 (64 requested) atoms. Cycle 10: After refmac, R = 0.2984 (Rfree = 0.000) for 4458 atoms. Found 29 (129 requested) and removed 19 (64 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.30 2.36 NCS extension: 17 residues added (0 deleted due to clashes), 4509 seeds are put forward Round 1: 312 peptides, 57 chains. Longest chain 15 peptides. Score 0.405 Round 2: 325 peptides, 53 chains. Longest chain 15 peptides. Score 0.479 Round 3: 329 peptides, 52 chains. Longest chain 15 peptides. Score 0.498 Round 4: 324 peptides, 53 chains. Longest chain 22 peptides. Score 0.477 Round 5: 323 peptides, 51 chains. Longest chain 16 peptides. Score 0.495 Taking the results from Round 3 Chains 52, Residues 277, Estimated correctness of the model 75.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9484 restraints for refining 4448 atoms. 8428 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3179 (Rfree = 0.000) for 4448 atoms. Found 94 (129 requested) and removed 48 (64 requested) atoms. Cycle 12: After refmac, R = 0.3026 (Rfree = 0.000) for 4491 atoms. Found 61 (130 requested) and removed 37 (65 requested) atoms. Cycle 13: After refmac, R = 0.2877 (Rfree = 0.000) for 4509 atoms. Found 51 (131 requested) and removed 33 (65 requested) atoms. Cycle 14: After refmac, R = 0.2785 (Rfree = 0.000) for 4524 atoms. Found 41 (131 requested) and removed 17 (65 requested) atoms. Cycle 15: After refmac, R = 0.2723 (Rfree = 0.000) for 4545 atoms. Found 33 (131 requested) and removed 15 (65 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.29 2.35 NCS extension: 9 residues added (1 deleted due to clashes), 4583 seeds are put forward Round 1: 275 peptides, 52 chains. Longest chain 14 peptides. Score 0.363 Round 2: 296 peptides, 50 chains. Longest chain 15 peptides. Score 0.440 Round 3: 282 peptides, 43 chains. Longest chain 16 peptides. Score 0.480 Round 4: 289 peptides, 48 chains. Longest chain 14 peptides. Score 0.444 Round 5: 319 peptides, 50 chains. Longest chain 17 peptides. Score 0.495 Taking the results from Round 5 Chains 50, Residues 269, Estimated correctness of the model 75.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9279 restraints for refining 4448 atoms. 8253 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3053 (Rfree = 0.000) for 4448 atoms. Found 98 (129 requested) and removed 45 (64 requested) atoms. Cycle 17: After refmac, R = 0.2883 (Rfree = 0.000) for 4498 atoms. Found 62 (130 requested) and removed 19 (65 requested) atoms. Cycle 18: After refmac, R = 0.2763 (Rfree = 0.000) for 4541 atoms. Found 51 (131 requested) and removed 14 (65 requested) atoms. Cycle 19: After refmac, R = 0.2694 (Rfree = 0.000) for 4574 atoms. Found 35 (132 requested) and removed 16 (66 requested) atoms. Cycle 20: After refmac, R = 0.2661 (Rfree = 0.000) for 4591 atoms. Found 33 (133 requested) and removed 17 (66 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.29 2.35 NCS extension: 13 residues added (1 deleted due to clashes), 4635 seeds are put forward Round 1: 278 peptides, 51 chains. Longest chain 14 peptides. Score 0.383 Round 2: 302 peptides, 47 chains. Longest chain 17 peptides. Score 0.486 Round 3: 310 peptides, 50 chains. Longest chain 24 peptides. Score 0.474 Round 4: 305 peptides, 47 chains. Longest chain 20 peptides. Score 0.493 Round 5: 303 peptides, 48 chains. Longest chain 20 peptides. Score 0.478 Taking the results from Round 4 Chains 47, Residues 258, Estimated correctness of the model 75.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9111 restraints for refining 4448 atoms. 8126 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2965 (Rfree = 0.000) for 4448 atoms. Found 111 (129 requested) and removed 37 (64 requested) atoms. Cycle 22: After refmac, R = 0.2818 (Rfree = 0.000) for 4521 atoms. Found 66 (131 requested) and removed 27 (65 requested) atoms. Cycle 23: After refmac, R = 0.2719 (Rfree = 0.000) for 4556 atoms. Found 59 (132 requested) and removed 12 (66 requested) atoms. Cycle 24: After refmac, R = 0.2645 (Rfree = 0.000) for 4599 atoms. Found 28 (133 requested) and removed 16 (66 requested) atoms. Cycle 25: After refmac, R = 0.2606 (Rfree = 0.000) for 4611 atoms. Found 23 (133 requested) and removed 9 (66 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.30 2.36 NCS extension: 17 residues added (1 deleted due to clashes), 4659 seeds are put forward Round 1: 263 peptides, 48 chains. Longest chain 13 peptides. Score 0.377 Round 2: 286 peptides, 46 chains. Longest chain 16 peptides. Score 0.458 Round 3: 294 peptides, 49 chains. Longest chain 15 peptides. Score 0.446 Round 4: 301 peptides, 47 chains. Longest chain 16 peptides. Score 0.484 Round 5: 287 peptides, 47 chains. Longest chain 17 peptides. Score 0.450 Taking the results from Round 4 Chains 49, Residues 254, Estimated correctness of the model 74.6 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 8895 restraints for refining 4469 atoms. 7834 conditional restraints added. Observations/parameters ratio is 1.95 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2936 (Rfree = 0.000) for 4469 atoms. Found 114 (129 requested) and removed 50 (64 requested) atoms. Cycle 27: After refmac, R = 0.2772 (Rfree = 0.000) for 4531 atoms. Found 58 (131 requested) and removed 16 (65 requested) atoms. Cycle 28: After refmac, R = 0.2670 (Rfree = 0.000) for 4572 atoms. Found 49 (132 requested) and removed 17 (66 requested) atoms. Cycle 29: After refmac, R = 0.2622 (Rfree = 0.000) for 4604 atoms. Found 25 (133 requested) and removed 9 (66 requested) atoms. Cycle 30: After refmac, R = 0.2572 (Rfree = 0.000) for 4620 atoms. Found 27 (134 requested) and removed 5 (67 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.29 2.35 NCS extension: 18 residues added (1 deleted due to clashes), 4674 seeds are put forward Round 1: 269 peptides, 46 chains. Longest chain 13 peptides. Score 0.415 Round 2: 291 peptides, 46 chains. Longest chain 17 peptides. Score 0.470 Round 3: 298 peptides, 45 chains. Longest chain 22 peptides. Score 0.497 Round 4: 289 peptides, 43 chains. Longest chain 17 peptides. Score 0.497 Round 5: 288 peptides, 44 chains. Longest chain 15 peptides. Score 0.484 Taking the results from Round 4 Chains 44, Residues 246, Estimated correctness of the model 75.7 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 8829 restraints for refining 4471 atoms. 7829 conditional restraints added. Observations/parameters ratio is 1.95 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2831 (Rfree = 0.000) for 4471 atoms. Found 106 (129 requested) and removed 46 (64 requested) atoms. Cycle 32: After refmac, R = 0.2698 (Rfree = 0.000) for 4530 atoms. Found 68 (131 requested) and removed 12 (65 requested) atoms. Cycle 33: After refmac, R = 0.2623 (Rfree = 0.000) for 4584 atoms. Found 48 (133 requested) and removed 7 (66 requested) atoms. Cycle 34: After refmac, R = 0.2531 (Rfree = 0.000) for 4625 atoms. Found 29 (134 requested) and removed 5 (67 requested) atoms. Cycle 35: After refmac, R = 0.2498 (Rfree = 0.000) for 4648 atoms. Found 36 (134 requested) and removed 5 (67 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.29 2.35 NCS extension: 14 residues added (0 deleted due to clashes), 4710 seeds are put forward Round 1: 248 peptides, 44 chains. Longest chain 13 peptides. Score 0.382 Round 2: 265 peptides, 41 chains. Longest chain 15 peptides. Score 0.460 Round 3: 269 peptides, 37 chains. Longest chain 20 peptides. Score 0.512 Round 4: 270 peptides, 41 chains. Longest chain 17 peptides. Score 0.472 Round 5: 284 peptides, 41 chains. Longest chain 17 peptides. Score 0.506 Taking the results from Round 3 Chains 37, Residues 232, Estimated correctness of the model 77.0 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 8951 restraints for refining 4590 atoms. 7938 conditional restraints added. Observations/parameters ratio is 1.90 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2741 (Rfree = 0.000) for 4590 atoms. Found 120 (133 requested) and removed 59 (66 requested) atoms. Cycle 37: After refmac, R = 0.2609 (Rfree = 0.000) for 4651 atoms. Found 66 (134 requested) and removed 14 (67 requested) atoms. Cycle 38: After refmac, R = 0.2516 (Rfree = 0.000) for 4702 atoms. Found 50 (136 requested) and removed 12 (68 requested) atoms. Cycle 39: After refmac, R = 0.2470 (Rfree = 0.000) for 4736 atoms. Found 44 (137 requested) and removed 9 (68 requested) atoms. Cycle 40: After refmac, R = 0.2430 (Rfree = 0.000) for 4767 atoms. Found 37 (138 requested) and removed 10 (69 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.29 2.35 NCS extension: 13 residues added (1 deleted due to clashes), 4821 seeds are put forward Round 1: 247 peptides, 42 chains. Longest chain 15 peptides. Score 0.403 Round 2: 246 peptides, 40 chains. Longest chain 17 peptides. Score 0.423 Round 3: 251 peptides, 36 chains. Longest chain 16 peptides. Score 0.480 Round 4: 245 peptides, 37 chains. Longest chain 16 peptides. Score 0.454 Round 5: 255 peptides, 39 chains. Longest chain 16 peptides. Score 0.457 Taking the results from Round 3 Chains 36, Residues 215, Estimated correctness of the model 74.2 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9310 restraints for refining 4612 atoms. 8440 conditional restraints added. Observations/parameters ratio is 1.89 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2704 (Rfree = 0.000) for 4612 atoms. Found 133 (133 requested) and removed 51 (66 requested) atoms. Cycle 42: After refmac, R = 0.2576 (Rfree = 0.000) for 4694 atoms. Found 74 (136 requested) and removed 15 (68 requested) atoms. Cycle 43: After refmac, R = 0.2503 (Rfree = 0.000) for 4752 atoms. Found 46 (137 requested) and removed 13 (68 requested) atoms. Cycle 44: After refmac, R = 0.2456 (Rfree = 0.000) for 4783 atoms. Found 38 (138 requested) and removed 9 (69 requested) atoms. Cycle 45: After refmac, R = 0.2428 (Rfree = 0.000) for 4812 atoms. Found 29 (139 requested) and removed 9 (69 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.29 2.35 NCS extension: 12 residues added (2 deleted due to clashes), 4851 seeds are put forward Round 1: 216 peptides, 38 chains. Longest chain 13 peptides. Score 0.365 Round 2: 247 peptides, 37 chains. Longest chain 16 peptides. Score 0.459 Round 3: 232 peptides, 38 chains. Longest chain 13 peptides. Score 0.409 Round 4: 245 peptides, 36 chains. Longest chain 19 peptides. Score 0.465 Round 5: 237 peptides, 34 chains. Longest chain 16 peptides. Score 0.467 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 203, Estimated correctness of the model 73.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2gfg-2_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 34827 reflections ( 98.30 % complete ) and 9267 restraints for refining 4618 atoms. 8489 conditional restraints added. Observations/parameters ratio is 1.89 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2706 (Rfree = 0.000) for 4618 atoms. Found 0 (133 requested) and removed 10 (66 requested) atoms. Cycle 47: After refmac, R = 0.2641 (Rfree = 0.000) for 4608 atoms. Found 0 (133 requested) and removed 2 (66 requested) atoms. Cycle 48: After refmac, R = 0.2609 (Rfree = 0.000) for 4606 atoms. Found 0 (133 requested) and removed 4 (66 requested) atoms. Cycle 49: After refmac, R = 0.2600 (Rfree = 0.000) for 4602 atoms. Found 0 (133 requested) and removed 4 (66 requested) atoms. Writing output files ... TimeTaking 46.65