Tue 25 Dec 19:27:57 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 2gb5-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gb5-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gb5-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gb5-3.8-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/2gb5-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gb5-3.8-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 19:28:06 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/2gb5-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gb5-3.8-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 381 and 0 Target number of residues in the AU: 381 Target solvent content: 0.6498 Checking the provided sequence file Detected sequence length: 269 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 538 Adjusted target solvent content: 0.51 Input MTZ file: 2gb5-3.8-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: 18 Cell parameters: 99.287 103.553 57.270 90.000 90.000 90.000 Input sequence file: 2gb5-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 4304 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: 49.644 3.800 Wilson plot Bfac: 77.61 6155 reflections ( 99.32 % complete ) and 0 restraints for refining 4781 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3331 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3295 (Rfree = 0.000) for 4781 atoms. Found 26 (26 requested) and removed 29 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.56 Search for helices and strands: 0 residues in 0 chains, 4839 seeds are put forward NCS extension: 0 residues added, 4839 seeds are put forward Round 1: 149 peptides, 32 chains. Longest chain 9 peptides. Score 0.241 Round 2: 215 peptides, 41 chains. Longest chain 9 peptides. Score 0.329 Round 3: 234 peptides, 39 chains. Longest chain 11 peptides. Score 0.407 Round 4: 252 peptides, 43 chains. Longest chain 14 peptides. Score 0.409 Round 5: 251 peptides, 41 chains. Longest chain 14 peptides. Score 0.429 Taking the results from Round 5 Chains 41, Residues 210, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 9249 restraints for refining 3892 atoms. 8450 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3107 (Rfree = 0.000) for 3892 atoms. Found 18 (21 requested) and removed 35 (10 requested) atoms. Cycle 2: After refmac, R = 0.2950 (Rfree = 0.000) for 3798 atoms. Found 14 (21 requested) and removed 34 (10 requested) atoms. Cycle 3: After refmac, R = 0.2561 (Rfree = 0.000) for 3738 atoms. Found 6 (20 requested) and removed 19 (10 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2728 (Rfree = 0.000) for 3704 atoms. Found 16 (20 requested) and removed 21 (10 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2752 (Rfree = 0.000) for 3679 atoms. Found 16 (20 requested) and removed 20 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 3.56 Search for helices and strands: 0 residues in 0 chains, 3751 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3766 seeds are put forward Round 1: 211 peptides, 40 chains. Longest chain 10 peptides. Score 0.330 Round 2: 234 peptides, 40 chains. Longest chain 15 peptides. Score 0.395 Round 3: 255 peptides, 42 chains. Longest chain 12 peptides. Score 0.428 Round 4: 236 peptides, 37 chains. Longest chain 16 peptides. Score 0.436 Round 5: 231 peptides, 38 chains. Longest chain 16 peptides. Score 0.411 Taking the results from Round 4 Chains 37, Residues 199, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 8786 restraints for refining 3755 atoms. 8027 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2828 (Rfree = 0.000) for 3755 atoms. Found 18 (20 requested) and removed 32 (10 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2803 (Rfree = 0.000) for 3694 atoms. Found 18 (20 requested) and removed 25 (10 requested) atoms. Cycle 8: After refmac, R = 0.2808 (Rfree = 0.000) for 3664 atoms. Found 18 (20 requested) and removed 25 (10 requested) atoms. Cycle 9: After refmac, R = 0.2525 (Rfree = 0.000) for 3633 atoms. Found 17 (20 requested) and removed 21 (10 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2535 (Rfree = 0.000) for 3610 atoms. Found 14 (19 requested) and removed 24 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.53 Search for helices and strands: 0 residues in 0 chains, 3706 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 3730 seeds are put forward Round 1: 194 peptides, 39 chains. Longest chain 12 peptides. Score 0.291 Round 2: 231 peptides, 35 chains. Longest chain 17 peptides. Score 0.446 Round 3: 242 peptides, 42 chains. Longest chain 14 peptides. Score 0.393 Round 4: 236 peptides, 38 chains. Longest chain 17 peptides. Score 0.424 Round 5: 242 peptides, 38 chains. Longest chain 16 peptides. Score 0.440 Taking the results from Round 2 Chains 35, Residues 196, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 8039 restraints for refining 3521 atoms. 7290 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2690 (Rfree = 0.000) for 3521 atoms. Found 19 (19 requested) and removed 30 (9 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2699 (Rfree = 0.000) for 3482 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 13: After refmac, R = 0.2609 (Rfree = 0.000) for 3467 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2529 (Rfree = 0.000) for 3452 atoms. Found 9 (19 requested) and removed 16 (9 requested) atoms. Cycle 15: After refmac, R = 0.2642 (Rfree = 0.000) for 3433 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.54 Search for helices and strands: 0 residues in 0 chains, 3529 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3551 seeds are put forward Round 1: 208 peptides, 43 chains. Longest chain 9 peptides. Score 0.283 Round 2: 221 peptides, 37 chains. Longest chain 12 peptides. Score 0.395 Round 3: 239 peptides, 40 chains. Longest chain 18 peptides. Score 0.409 Round 4: 247 peptides, 38 chains. Longest chain 17 peptides. Score 0.453 Round 5: 251 peptides, 38 chains. Longest chain 18 peptides. Score 0.463 Taking the results from Round 5 Chains 38, Residues 213, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 8354 restraints for refining 3665 atoms. 7540 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2784 (Rfree = 0.000) for 3665 atoms. Found 20 (20 requested) and removed 33 (10 requested) atoms. Cycle 17: After refmac, R = 0.2730 (Rfree = 0.000) for 3631 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2697 (Rfree = 0.000) for 3606 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2559 (Rfree = 0.000) for 3589 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2494 (Rfree = 0.000) for 3573 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 3675 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 3702 seeds are put forward Round 1: 191 peptides, 41 chains. Longest chain 11 peptides. Score 0.256 Round 2: 202 peptides, 37 chains. Longest chain 11 peptides. Score 0.341 Round 3: 197 peptides, 33 chains. Longest chain 17 peptides. Score 0.377 Round 4: 199 peptides, 30 chains. Longest chain 20 peptides. Score 0.420 Round 5: 195 peptides, 33 chains. Longest chain 14 peptides. Score 0.371 Taking the results from Round 4 Chains 31, Residues 169, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 8865 restraints for refining 3812 atoms. 8179 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2734 (Rfree = 0.000) for 3812 atoms. Found 20 (20 requested) and removed 35 (10 requested) atoms. Cycle 22: After refmac, R = 0.2601 (Rfree = 0.000) for 3772 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 23: After refmac, R = 0.2516 (Rfree = 0.000) for 3743 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 24: After refmac, R = 0.2517 (Rfree = 0.000) for 3729 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 25: After refmac, R = 0.2507 (Rfree = 0.000) for 3706 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 3.60 Search for helices and strands: 0 residues in 0 chains, 3784 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3808 seeds are put forward Round 1: 181 peptides, 41 chains. Longest chain 8 peptides. Score 0.224 Round 2: 217 peptides, 44 chains. Longest chain 15 peptides. Score 0.297 Round 3: 206 peptides, 44 chains. Longest chain 8 peptides. Score 0.264 Round 4: 198 peptides, 38 chains. Longest chain 10 peptides. Score 0.316 Round 5: 201 peptides, 38 chains. Longest chain 10 peptides. Score 0.325 Taking the results from Round 5 Chains 38, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6155 reflections ( 99.32 % complete ) and 8830 restraints for refining 3757 atoms. 8216 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2718 (Rfree = 0.000) for 3757 atoms. Found 20 (20 requested) and removed 30 (10 requested) atoms. Cycle 27: After refmac, R = 0.2753 (Rfree = 0.000) for 3714 atoms. Found 20 (20 requested) and removed 26 (10 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2614 (Rfree = 0.000) for 3676 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 29: After refmac, R = 0.2580 (Rfree = 0.000) for 3656 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. Cycle 30: After refmac, R = 0.2782 (Rfree = 0.000) for 3637 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 3.52 Search for helices and strands: 0 residues in 0 chains, 3725 seeds are put forward NCS extension: 0 residues added, 3725 seeds are put forward Round 1: 139 peptides, 32 chains. Longest chain 6 peptides. Score 0.207 Round 2: 169 peptides, 35 chains. Longest chain 8 peptides. Score 0.266 Round 3: 170 peptides, 31 chains. Longest chain 11 peptides. Score 0.323 Round 4: 172 peptides, 33 chains. Longest chain 10 peptides. Score 0.302 Round 5: 183 peptides, 31 chains. Longest chain 10 peptides. Score 0.362 Taking the results from Round 5 Chains 31, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6155 reflections ( 99.32 % complete ) and 8349 restraints for refining 3646 atoms. 7772 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2836 (Rfree = 0.000) for 3646 atoms. Found 20 (20 requested) and removed 28 (10 requested) atoms. Cycle 32: After refmac, R = 0.2719 (Rfree = 0.000) for 3608 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2654 (Rfree = 0.000) for 3594 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 34: After refmac, R = 0.2634 (Rfree = 0.000) for 3570 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. Cycle 35: After refmac, R = 0.2747 (Rfree = 0.000) for 3558 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.53 Search for helices and strands: 0 residues in 0 chains, 3605 seeds are put forward NCS extension: 0 residues added, 3605 seeds are put forward Round 1: 135 peptides, 29 chains. Longest chain 9 peptides. Score 0.236 Round 2: 176 peptides, 36 chains. Longest chain 10 peptides. Score 0.275 Round 3: 193 peptides, 36 chains. Longest chain 11 peptides. Score 0.327 Round 4: 204 peptides, 40 chains. Longest chain 11 peptides. Score 0.309 Round 5: 195 peptides, 36 chains. Longest chain 10 peptides. Score 0.333 Taking the results from Round 5 Chains 36, Residues 159, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 8397 restraints for refining 3569 atoms. 7797 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2985 (Rfree = 0.000) for 3569 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 37: After refmac, R = 0.2689 (Rfree = 0.000) for 3535 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 38: After refmac, R = 0.2564 (Rfree = 0.000) for 3520 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 39: After refmac, R = 0.2663 (Rfree = 0.000) for 3512 atoms. Found 19 (19 requested) and removed 41 (9 requested) atoms. Cycle 40: After refmac, R = 0.2547 (Rfree = 0.000) for 3484 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.55 Search for helices and strands: 0 residues in 0 chains, 3535 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3546 seeds are put forward Round 1: 155 peptides, 33 chains. Longest chain 10 peptides. Score 0.247 Round 2: 179 peptides, 37 chains. Longest chain 10 peptides. Score 0.271 Round 3: 177 peptides, 34 chains. Longest chain 10 peptides. Score 0.304 Round 4: 192 peptides, 34 chains. Longest chain 12 peptides. Score 0.350 Round 5: 197 peptides, 34 chains. Longest chain 14 peptides. Score 0.364 Taking the results from Round 5 Chains 34, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 8243 restraints for refining 3591 atoms. 7625 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2581 (Rfree = 0.000) for 3591 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. Cycle 42: After refmac, R = 0.2637 (Rfree = 0.000) for 3569 atoms. Found 19 (19 requested) and removed 30 (9 requested) atoms. Cycle 43: After refmac, R = 0.2539 (Rfree = 0.000) for 3538 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 44: After refmac, R = 0.2375 (Rfree = 0.000) for 3533 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 45: After refmac, R = 0.2389 (Rfree = 0.000) for 3527 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.54 Search for helices and strands: 0 residues in 0 chains, 3614 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3632 seeds are put forward Round 1: 124 peptides, 28 chains. Longest chain 7 peptides. Score 0.212 Round 2: 136 peptides, 28 chains. Longest chain 7 peptides. Score 0.254 Round 3: 146 peptides, 27 chains. Longest chain 10 peptides. Score 0.302 Round 4: 151 peptides, 25 chains. Longest chain 12 peptides. Score 0.346 Round 5: 170 peptides, 32 chains. Longest chain 14 peptides. Score 0.309 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2gb5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6155 reflections ( 99.32 % complete ) and 8019 restraints for refining 3469 atoms. 7540 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2684 (Rfree = 0.000) for 3469 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2697 (Rfree = 0.000) for 3443 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2630 (Rfree = 0.000) for 3419 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2646 (Rfree = 0.000) for 3402 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Writing output files ... TimeTaking 60.9