Tue 25 Dec 19:27:55 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 2gfg-2.1-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gfg-2.1-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gfg-2.1-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gfg-2.1-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/2gfg-2.1-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gfg-2.1-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 ============================================================ Tue 25 Dec 19:28:04 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/2gfg-2.1-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gfg-2.1-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 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-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: 43.030 74.690 188.130 90.000 90.000 90.000 Input sequence file: 2gfg-2.1-parrot-hancs.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 5095 atoms. Observations/parameters ratio is 1.71 ------------------------------------------------------ Starting model: R = 0.3949 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3409 (Rfree = 0.000) for 5095 atoms. Found 81 (147 requested) and removed 93 (73 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.36 2.42 NCS extension: 0 residues added, 5083 seeds are put forward Round 1: 219 peptides, 46 chains. Longest chain 11 peptides. Score 0.276 Round 2: 255 peptides, 47 chains. Longest chain 11 peptides. Score 0.366 Round 3: 273 peptides, 44 chains. Longest chain 16 peptides. Score 0.447 Round 4: 289 peptides, 45 chains. Longest chain 18 peptides. Score 0.476 Round 5: 293 peptides, 47 chains. Longest chain 17 peptides. Score 0.465 Taking the results from Round 4 Chains 45, Residues 244, Estimated correctness of the model 73.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9622 restraints for refining 4447 atoms. 8691 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3603 (Rfree = 0.000) for 4447 atoms. Found 101 (129 requested) and removed 68 (64 requested) atoms. Cycle 2: After refmac, R = 0.3370 (Rfree = 0.000) for 4468 atoms. Found 85 (129 requested) and removed 65 (64 requested) atoms. Cycle 3: After refmac, R = 0.3202 (Rfree = 0.000) for 4480 atoms. Found 58 (130 requested) and removed 43 (65 requested) atoms. Cycle 4: After refmac, R = 0.3090 (Rfree = 0.000) for 4484 atoms. Found 40 (130 requested) and removed 28 (65 requested) atoms. Cycle 5: After refmac, R = 0.2991 (Rfree = 0.000) for 4492 atoms. Found 33 (130 requested) and removed 10 (65 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.29 2.35 NCS extension: 20 residues added (3 deleted due to clashes), 4571 seeds are put forward Round 1: 276 peptides, 54 chains. Longest chain 9 peptides. Score 0.343 Round 2: 295 peptides, 48 chains. Longest chain 18 peptides. Score 0.459 Round 3: 314 peptides, 49 chains. Longest chain 21 peptides. Score 0.494 Round 4: 317 peptides, 50 chains. Longest chain 12 peptides. Score 0.491 Round 5: 324 peptides, 54 chains. Longest chain 12 peptides. Score 0.467 Taking the results from Round 3 Chains 49, Residues 265, Estimated correctness of the model 75.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9620 restraints for refining 4448 atoms. 8609 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3229 (Rfree = 0.000) for 4448 atoms. Found 102 (129 requested) and removed 61 (64 requested) atoms. Cycle 7: After refmac, R = 0.3062 (Rfree = 0.000) for 4486 atoms. Found 65 (130 requested) and removed 35 (65 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2941 (Rfree = 0.000) for 4514 atoms. Found 37 (131 requested) and removed 25 (65 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2862 (Rfree = 0.000) for 4523 atoms. Found 44 (131 requested) and removed 15 (65 requested) atoms. Cycle 10: After refmac, R = 0.2783 (Rfree = 0.000) for 4549 atoms. Found 37 (132 requested) and removed 15 (66 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.29 2.35 NCS extension: 21 residues added (4 deleted due to clashes), 4609 seeds are put forward Round 1: 252 peptides, 49 chains. Longest chain 9 peptides. Score 0.335 Round 2: 282 peptides, 47 chains. Longest chain 11 peptides. Score 0.437 Round 3: 282 peptides, 46 chains. Longest chain 12 peptides. Score 0.448 Round 4: 275 peptides, 45 chains. Longest chain 18 peptides. Score 0.441 Round 5: 268 peptides, 43 chains. Longest chain 18 peptides. Score 0.446 Taking the results from Round 3 Chains 46, Residues 236, Estimated correctness of the model 71.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9732 restraints for refining 4448 atoms. 8834 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3056 (Rfree = 0.000) for 4448 atoms. Found 120 (129 requested) and removed 53 (64 requested) atoms. Cycle 12: After refmac, R = 0.2869 (Rfree = 0.000) for 4514 atoms. Found 47 (131 requested) and removed 29 (65 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2760 (Rfree = 0.000) for 4531 atoms. Found 41 (131 requested) and removed 16 (65 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2692 (Rfree = 0.000) for 4554 atoms. Found 32 (132 requested) and removed 12 (66 requested) atoms. Cycle 15: After refmac, R = 0.2652 (Rfree = 0.000) for 4567 atoms. Found 26 (132 requested) and removed 9 (66 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.29 2.35 NCS extension: 11 residues added (0 deleted due to clashes), 4614 seeds are put forward Round 1: 262 peptides, 48 chains. Longest chain 12 peptides. Score 0.374 Round 2: 269 peptides, 43 chains. Longest chain 13 peptides. Score 0.448 Round 3: 268 peptides, 47 chains. Longest chain 14 peptides. Score 0.401 Round 4: 287 peptides, 47 chains. Longest chain 14 peptides. Score 0.450 Round 5: 282 peptides, 48 chains. Longest chain 11 peptides. Score 0.426 Taking the results from Round 4 Chains 47, Residues 240, Estimated correctness of the model 71.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 34827 reflections ( 98.30 % complete ) and 9320 restraints for refining 4448 atoms. 8407 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3027 (Rfree = 0.000) for 4448 atoms. Found 118 (129 requested) and removed 40 (64 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2856 (Rfree = 0.000) for 4525 atoms. Found 62 (131 requested) and removed 21 (65 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2739 (Rfree = 0.000) for 4564 atoms. Found 40 (132 requested) and removed 19 (66 requested) atoms. Cycle 19: After refmac, R = 0.2682 (Rfree = 0.000) for 4582 atoms. Found 40 (133 requested) and removed 12 (66 requested) atoms. Cycle 20: After refmac, R = 0.2627 (Rfree = 0.000) for 4609 atoms. Found 27 (133 requested) and removed 10 (66 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.28 2.34 NCS extension: 10 residues added (1 deleted due to clashes), 4662 seeds are put forward Round 1: 257 peptides, 51 chains. Longest chain 13 peptides. Score 0.325 Round 2: 271 peptides, 50 chains. Longest chain 11 peptides. Score 0.375 Round 3: 274 peptides, 47 chains. Longest chain 14 peptides. Score 0.417 Round 4: 279 peptides, 51 chains. Longest chain 13 peptides. Score 0.385 Round 5: 272 peptides, 47 chains. Longest chain 13 peptides. Score 0.412 Taking the results from Round 3 Chains 47, Residues 227, Estimated correctness of the model 68.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9190 restraints for refining 4448 atoms. 8329 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2858 (Rfree = 0.000) for 4448 atoms. Found 120 (129 requested) and removed 29 (64 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2717 (Rfree = 0.000) for 4539 atoms. Found 78 (131 requested) and removed 18 (65 requested) atoms. Cycle 23: After refmac, R = 0.2623 (Rfree = 0.000) for 4597 atoms. Found 59 (133 requested) and removed 16 (66 requested) atoms. Cycle 24: After refmac, R = 0.2576 (Rfree = 0.000) for 4637 atoms. Found 52 (134 requested) and removed 10 (67 requested) atoms. Cycle 25: After refmac, R = 0.2550 (Rfree = 0.000) for 4677 atoms. Found 50 (135 requested) and removed 20 (67 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.29 2.35 NCS extension: 17 residues added (1 deleted due to clashes), 4748 seeds are put forward Round 1: 259 peptides, 45 chains. Longest chain 13 peptides. Score 0.400 Round 2: 277 peptides, 43 chains. Longest chain 15 peptides. Score 0.468 Round 3: 275 peptides, 44 chains. Longest chain 13 peptides. Score 0.452 Round 4: 271 peptides, 39 chains. Longest chain 22 peptides. Score 0.496 Round 5: 269 peptides, 41 chains. Longest chain 15 peptides. Score 0.470 Taking the results from Round 4 Chains 40, Residues 232, Estimated correctness of the model 75.6 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 34827 reflections ( 98.30 % complete ) and 9024 restraints for refining 4495 atoms. 8099 conditional restraints added. Observations/parameters ratio is 1.94 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2863 (Rfree = 0.000) for 4495 atoms. Found 130 (130 requested) and removed 55 (65 requested) atoms. Cycle 27: After refmac, R = 0.2732 (Rfree = 0.000) for 4566 atoms. Found 102 (132 requested) and removed 28 (66 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2652 (Rfree = 0.000) for 4636 atoms. Found 76 (134 requested) and removed 32 (67 requested) atoms. Cycle 29: After refmac, R = 0.2620 (Rfree = 0.000) for 4677 atoms. Found 72 (135 requested) and removed 27 (67 requested) atoms. Cycle 30: After refmac, R = 0.2572 (Rfree = 0.000) for 4722 atoms. Found 64 (137 requested) and removed 30 (68 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.28 2.34 NCS extension: 10 residues added (2 deleted due to clashes), 4792 seeds are put forward Round 1: 235 peptides, 39 chains. Longest chain 18 peptides. Score 0.405 Round 2: 240 peptides, 36 chains. Longest chain 15 peptides. Score 0.453 Round 3: 256 peptides, 38 chains. Longest chain 24 peptides. Score 0.470 Round 4: 244 peptides, 38 chains. Longest chain 14 peptides. Score 0.440 Round 5: 256 peptides, 39 chains. Longest chain 12 peptides. Score 0.460 Taking the results from Round 3 Chains 38, Residues 218, Estimated correctness of the model 73.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9237 restraints for refining 4502 atoms. 8403 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2727 (Rfree = 0.000) for 4502 atoms. Found 130 (130 requested) and removed 30 (65 requested) atoms. Cycle 32: After refmac, R = 0.2594 (Rfree = 0.000) for 4599 atoms. Found 86 (133 requested) and removed 16 (66 requested) atoms. Cycle 33: After refmac, R = 0.2528 (Rfree = 0.000) for 4668 atoms. Found 60 (135 requested) and removed 33 (67 requested) atoms. Cycle 34: After refmac, R = 0.2475 (Rfree = 0.000) for 4694 atoms. Found 73 (136 requested) and removed 20 (68 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2432 (Rfree = 0.000) for 4747 atoms. Found 59 (137 requested) and removed 31 (68 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.28 2.34 NCS extension: 29 residues added (2 deleted due to clashes), 4822 seeds are put forward Round 1: 206 peptides, 35 chains. Longest chain 17 peptides. Score 0.374 Round 2: 205 peptides, 34 chains. Longest chain 13 peptides. Score 0.383 Round 3: 207 peptides, 33 chains. Longest chain 15 peptides. Score 0.401 Round 4: 216 peptides, 32 chains. Longest chain 22 peptides. Score 0.437 Round 5: 221 peptides, 35 chains. Longest chain 13 peptides. Score 0.415 Taking the results from Round 4 Chains 33, Residues 184, Estimated correctness of the model 70.2 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9400 restraints for refining 4596 atoms. 8611 conditional restraints added. Observations/parameters ratio is 1.89 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2709 (Rfree = 0.000) for 4596 atoms. Found 133 (133 requested) and removed 49 (66 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2498 (Rfree = 0.000) for 4680 atoms. Found 94 (135 requested) and removed 16 (67 requested) atoms. Cycle 38: After refmac, R = 0.2417 (Rfree = 0.000) for 4756 atoms. Found 70 (138 requested) and removed 18 (69 requested) atoms. Cycle 39: After refmac, R = 0.2358 (Rfree = 0.000) for 4808 atoms. Found 64 (139 requested) and removed 19 (69 requested) atoms. Cycle 40: After refmac, R = 0.2316 (Rfree = 0.000) for 4852 atoms. Found 60 (140 requested) and removed 26 (70 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.27 2.33 NCS extension: 28 residues added (1 deleted due to clashes), 4925 seeds are put forward Round 1: 214 peptides, 35 chains. Longest chain 12 peptides. Score 0.396 Round 2: 219 peptides, 36 chains. Longest chain 15 peptides. Score 0.398 Round 3: 238 peptides, 40 chains. Longest chain 14 peptides. Score 0.402 Round 4: 232 peptides, 37 chains. Longest chain 18 peptides. Score 0.421 Round 5: 233 peptides, 37 chains. Longest chain 15 peptides. Score 0.423 Taking the results from Round 5 Chains 37, Residues 196, Estimated correctness of the model 68.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9432 restraints for refining 4614 atoms. 8685 conditional restraints added. Observations/parameters ratio is 1.89 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2631 (Rfree = 0.000) for 4614 atoms. Found 133 (133 requested) and removed 25 (66 requested) atoms. Cycle 42: After refmac, R = 0.2486 (Rfree = 0.000) for 4722 atoms. Found 93 (137 requested) and removed 23 (68 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2389 (Rfree = 0.000) for 4790 atoms. Found 73 (139 requested) and removed 21 (69 requested) atoms. Cycle 44: After refmac, R = 0.2333 (Rfree = 0.000) for 4841 atoms. Found 58 (140 requested) and removed 24 (70 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.2289 (Rfree = 0.000) for 4874 atoms. Found 64 (141 requested) and removed 30 (70 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.27 2.33 NCS extension: 9 residues added (0 deleted due to clashes), 4923 seeds are put forward Round 1: 215 peptides, 40 chains. Longest chain 13 peptides. Score 0.338 Round 2: 224 peptides, 37 chains. Longest chain 26 peptides. Score 0.399 Round 3: 228 peptides, 35 chains. Longest chain 26 peptides. Score 0.433 Round 4: 204 peptides, 33 chains. Longest chain 18 peptides. Score 0.393 Round 5: 219 peptides, 36 chains. Longest chain 13 peptides. Score 0.398 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 193, Estimated correctness of the model 69.8 % 1 chains (23 residues) have been docked in sequence Sequence coverage is 11 % 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 9610 restraints for refining 4723 atoms. 8775 conditional restraints added. Observations/parameters ratio is 1.84 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2575 (Rfree = 0.000) for 4723 atoms. Found 0 (137 requested) and removed 17 (68 requested) atoms. Cycle 47: After refmac, R = 0.2491 (Rfree = 0.000) for 4706 atoms. Found 0 (136 requested) and removed 0 (68 requested) atoms. Cycle 48: After refmac, R = 0.2451 (Rfree = 0.000) for 4704 atoms. Found 0 (136 requested) and removed 4 (68 requested) atoms. Cycle 49: After refmac, R = 0.2434 (Rfree = 0.000) for 4700 atoms. Found 0 (136 requested) and removed 4 (68 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:36:04 GMT 2018 Job finished. Failed to save intermediate PDB TimeTaking 68.15