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 2o5r-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o5r-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o5r-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o5r-3.4-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/2o5r-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o5r-3.4-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 19:28:07 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/2o5r-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o5r-3.4-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 484 and 0 Target number of residues in the AU: 484 Target solvent content: 0.6735 Checking the provided sequence file Detected sequence length: 481 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 481 Adjusted target solvent content: 0.68 Input MTZ file: 2o5r-3.4-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: 152 Cell parameters: 69.953 69.953 283.945 90.000 90.000 120.000 Input sequence file: 2o5r-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3848 target number of atoms Had to go as low as 1.00 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 Loops will be built when appropriate and at the last cycle Resolution range: 19.992 3.400 Wilson plot Bfac: 95.31 11761 reflections ( 99.27 % complete ) and 0 restraints for refining 4295 atoms. Observations/parameters ratio is 0.68 ------------------------------------------------------ Starting model: R = 0.3468 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3386 (Rfree = 0.000) for 4295 atoms. Found 32 (32 requested) and removed 33 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.78 2.94 Search for helices and strands: 0 residues in 0 chains, 4401 seeds are put forward Round 1: 210 peptides, 35 chains. Longest chain 15 peptides. Score 0.346 Round 2: 283 peptides, 38 chains. Longest chain 15 peptides. Score 0.469 Round 3: 304 peptides, 36 chains. Longest chain 18 peptides. Score 0.524 Round 4: 314 peptides, 35 chains. Longest chain 23 peptides. Score 0.549 Round 5: 299 peptides, 33 chains. Longest chain 22 peptides. Score 0.540 Taking the results from Round 4 Chains 37, Residues 279, Estimated correctness of the model 11.2 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 11761 reflections ( 99.27 % complete ) and 7528 restraints for refining 3499 atoms. 6331 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3143 (Rfree = 0.000) for 3499 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. Cycle 2: After refmac, R = 0.3009 (Rfree = 0.000) for 3427 atoms. Found 26 (26 requested) and removed 26 (13 requested) atoms. Cycle 3: After refmac, R = 0.2871 (Rfree = 0.000) for 3392 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. Cycle 4: After refmac, R = 0.2757 (Rfree = 0.000) for 3375 atoms. Found 21 (25 requested) and removed 15 (12 requested) atoms. Cycle 5: After refmac, R = 0.2701 (Rfree = 0.000) for 3370 atoms. Found 20 (25 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.78 2.94 Search for helices and strands: 0 residues in 0 chains, 3506 seeds are put forward Round 1: 302 peptides, 36 chains. Longest chain 28 peptides. Score 0.521 Round 2: 309 peptides, 34 chains. Longest chain 27 peptides. Score 0.549 Round 3: 325 peptides, 33 chains. Longest chain 44 peptides. Score 0.583 Round 4: 333 peptides, 31 chains. Longest chain 44 peptides. Score 0.610 Round 5: 324 peptides, 34 chains. Longest chain 19 peptides. Score 0.574 Taking the results from Round 4 Chains 32, Residues 302, Estimated correctness of the model 31.9 % 2 chains (62 residues) have been docked in sequence ------------------------------------------------------ 11761 reflections ( 99.27 % complete ) and 6680 restraints for refining 3499 atoms. 5204 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2963 (Rfree = 0.000) for 3499 atoms. Found 26 (26 requested) and removed 36 (13 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2801 (Rfree = 0.000) for 3438 atoms. Found 26 (26 requested) and removed 25 (13 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2706 (Rfree = 0.000) for 3410 atoms. Found 18 (25 requested) and removed 22 (12 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2628 (Rfree = 0.000) for 3381 atoms. Found 20 (25 requested) and removed 18 (12 requested) atoms. Cycle 10: After refmac, R = 0.2608 (Rfree = 0.000) for 3364 atoms. Found 16 (25 requested) and removed 21 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.75 2.92 Search for helices and strands: 0 residues in 0 chains, 3520 seeds are put forward Round 1: 291 peptides, 41 chains. Longest chain 17 peptides. Score 0.458 Round 2: 317 peptides, 34 chains. Longest chain 24 peptides. Score 0.562 Round 3: 308 peptides, 33 chains. Longest chain 27 peptides. Score 0.555 Round 4: 307 peptides, 32 chains. Longest chain 28 peptides. Score 0.561 Round 5: 301 peptides, 30 chains. Longest chain 25 peptides. Score 0.567 Taking the results from Round 5 Chains 33, Residues 271, Estimated correctness of the model 17.5 % 3 chains (53 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 11761 reflections ( 99.27 % complete ) and 6998 restraints for refining 3498 atoms. 5679 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2904 (Rfree = 0.000) for 3498 atoms. Found 26 (26 requested) and removed 25 (13 requested) atoms. Cycle 12: After refmac, R = 0.2809 (Rfree = 0.000) for 3451 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. Cycle 13: After refmac, R = 0.2681 (Rfree = 0.000) for 3431 atoms. Found 18 (26 requested) and removed 24 (13 requested) atoms. Cycle 14: After refmac, R = 0.2632 (Rfree = 0.000) for 3410 atoms. Found 13 (25 requested) and removed 17 (12 requested) atoms. Cycle 15: After refmac, R = 0.2483 (Rfree = 0.000) for 3391 atoms. Found 8 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.75 2.92 Search for helices and strands: 0 residues in 0 chains, 3520 seeds are put forward Round 1: 292 peptides, 38 chains. Longest chain 14 peptides. Score 0.486 Round 2: 304 peptides, 31 chains. Longest chain 24 peptides. Score 0.564 Round 3: 314 peptides, 33 chains. Longest chain 25 peptides. Score 0.565 Round 4: 304 peptides, 32 chains. Longest chain 23 peptides. Score 0.556 Round 5: 308 peptides, 40 chains. Longest chain 24 peptides. Score 0.498 Taking the results from Round 3 Chains 37, Residues 281, Estimated correctness of the model 16.8 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 11761 reflections ( 99.27 % complete ) and 7160 restraints for refining 3497 atoms. 5944 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2818 (Rfree = 0.000) for 3497 atoms. Found 25 (26 requested) and removed 26 (13 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2755 (Rfree = 0.000) for 3475 atoms. Found 21 (26 requested) and removed 24 (13 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2753 (Rfree = 0.000) for 3446 atoms. Found 26 (26 requested) and removed 25 (13 requested) atoms. Cycle 19: After refmac, R = 0.2674 (Rfree = 0.000) for 3435 atoms. Found 21 (26 requested) and removed 23 (13 requested) atoms. Cycle 20: After refmac, R = 0.2648 (Rfree = 0.000) for 3418 atoms. Found 21 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.75 2.92 Search for helices and strands: 0 residues in 0 chains, 3625 seeds are put forward Round 1: 283 peptides, 46 chains. Longest chain 14 peptides. Score 0.398 Round 2: 304 peptides, 40 chains. Longest chain 16 peptides. Score 0.491 Round 3: 300 peptides, 40 chains. Longest chain 16 peptides. Score 0.483 Round 4: 294 peptides, 35 chains. Longest chain 18 peptides. Score 0.515 Round 5: 297 peptides, 34 chains. Longest chain 24 peptides. Score 0.528 Taking the results from Round 5 Chains 35, Residues 263, Estimated correctness of the model 3.4 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 11761 reflections ( 99.27 % complete ) and 7566 restraints for refining 3498 atoms. 6498 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2797 (Rfree = 0.000) for 3498 atoms. Found 26 (26 requested) and removed 27 (13 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2736 (Rfree = 0.000) for 3471 atoms. Found 19 (26 requested) and removed 26 (13 requested) atoms. Cycle 23: After refmac, R = 0.2718 (Rfree = 0.000) for 3447 atoms. Found 21 (26 requested) and removed 23 (13 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2662 (Rfree = 0.000) for 3425 atoms. Found 24 (26 requested) and removed 21 (13 requested) atoms. Cycle 25: After refmac, R = 0.2610 (Rfree = 0.000) for 3415 atoms. Found 23 (25 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.70 2.88 Search for helices and strands: 0 residues in 0 chains, 3585 seeds are put forward Round 1: 284 peptides, 48 chains. Longest chain 13 peptides. Score 0.382 Round 2: 299 peptides, 37 chains. Longest chain 25 peptides. Score 0.507 Round 3: 305 peptides, 39 chains. Longest chain 19 peptides. Score 0.501 Round 4: 310 peptides, 43 chains. Longest chain 16 peptides. Score 0.477 Round 5: 311 peptides, 39 chains. Longest chain 18 peptides. Score 0.512 Taking the results from Round 5 Chains 39, Residues 272, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 11761 reflections ( 99.27 % complete ) and 7485 restraints for refining 3499 atoms. 6436 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2902 (Rfree = 0.000) for 3499 atoms. Found 26 (26 requested) and removed 25 (13 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2764 (Rfree = 0.000) for 3459 atoms. Found 26 (26 requested) and removed 18 (13 requested) atoms. Cycle 28: After refmac, R = 0.2688 (Rfree = 0.000) for 3448 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2689 (Rfree = 0.000) for 3438 atoms. Found 26 (26 requested) and removed 21 (13 requested) atoms. Cycle 30: After refmac, R = 0.2587 (Rfree = 0.000) for 3434 atoms. Found 25 (25 requested) and removed 21 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.73 2.90 Search for helices and strands: 0 residues in 0 chains, 3622 seeds are put forward Round 1: 257 peptides, 42 chains. Longest chain 20 peptides. Score 0.381 Round 2: 288 peptides, 35 chains. Longest chain 22 peptides. Score 0.504 Round 3: 280 peptides, 34 chains. Longest chain 25 peptides. Score 0.498 Round 4: 296 peptides, 36 chains. Longest chain 23 peptides. Score 0.510 Round 5: 300 peptides, 35 chains. Longest chain 23 peptides. Score 0.525 Taking the results from Round 5 Chains 36, Residues 265, Estimated correctness of the model 2.3 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ 11761 reflections ( 99.27 % complete ) and 7169 restraints for refining 3499 atoms. 5971 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2913 (Rfree = 0.000) for 3499 atoms. Found 26 (26 requested) and removed 20 (13 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2818 (Rfree = 0.000) for 3482 atoms. Found 26 (26 requested) and removed 20 (13 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2753 (Rfree = 0.000) for 3470 atoms. Found 26 (26 requested) and removed 20 (13 requested) atoms. Cycle 34: After refmac, R = 0.2713 (Rfree = 0.000) for 3456 atoms. Found 26 (26 requested) and removed 18 (13 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2696 (Rfree = 0.000) for 3453 atoms. Found 26 (26 requested) and removed 22 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.78 2.94 Search for helices and strands: 0 residues in 0 chains, 3617 seeds are put forward Round 1: 263 peptides, 42 chains. Longest chain 18 peptides. Score 0.393 Round 2: 293 peptides, 41 chains. Longest chain 19 peptides. Score 0.462 Round 3: 286 peptides, 39 chains. Longest chain 25 peptides. Score 0.466 Round 4: 276 peptides, 35 chains. Longest chain 24 peptides. Score 0.482 Round 5: 281 peptides, 31 chains. Longest chain 25 peptides. Score 0.525 Taking the results from Round 5 Chains 34, Residues 250, Estimated correctness of the model 2.3 % 6 chains (87 residues) have been docked in sequence ------------------------------------------------------ 11761 reflections ( 99.27 % complete ) and 6815 restraints for refining 3498 atoms. 5475 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2909 (Rfree = 0.000) for 3498 atoms. Found 26 (26 requested) and removed 34 (13 requested) atoms. Cycle 37: After refmac, R = 0.2782 (Rfree = 0.000) for 3458 atoms. Found 24 (26 requested) and removed 19 (13 requested) atoms. Cycle 38: After refmac, R = 0.2741 (Rfree = 0.000) for 3447 atoms. Found 23 (26 requested) and removed 25 (13 requested) atoms. Cycle 39: After refmac, R = 0.2676 (Rfree = 0.000) for 3430 atoms. Found 24 (26 requested) and removed 20 (13 requested) atoms. Cycle 40: After refmac, R = 0.2670 (Rfree = 0.000) for 3429 atoms. Found 21 (25 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 2.88 Search for helices and strands: 0 residues in 0 chains, 3585 seeds are put forward Round 1: 258 peptides, 41 chains. Longest chain 16 peptides. Score 0.392 Round 2: 290 peptides, 41 chains. Longest chain 19 peptides. Score 0.456 Round 3: 289 peptides, 34 chains. Longest chain 21 peptides. Score 0.514 Round 4: 282 peptides, 36 chains. Longest chain 18 peptides. Score 0.484 Round 5: 282 peptides, 41 chains. Longest chain 19 peptides. Score 0.441 Taking the results from Round 3 Chains 34, Residues 255, Estimated correctness of the model 0.0 % 4 chains (54 residues) have been docked in sequence ------------------------------------------------------ 11761 reflections ( 99.27 % complete ) and 7065 restraints for refining 3499 atoms. 5854 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2979 (Rfree = 0.000) for 3499 atoms. Found 26 (26 requested) and removed 23 (13 requested) atoms. Cycle 42: After refmac, R = 0.2871 (Rfree = 0.000) for 3474 atoms. Found 26 (26 requested) and removed 17 (13 requested) atoms. Cycle 43: After refmac, R = 0.2883 (Rfree = 0.000) for 3465 atoms. Found 26 (26 requested) and removed 21 (13 requested) atoms. Cycle 44: After refmac, R = 0.2787 (Rfree = 0.000) for 3462 atoms. Found 26 (26 requested) and removed 24 (13 requested) atoms. Cycle 45: After refmac, R = 0.2833 (Rfree = 0.000) for 3452 atoms. Found 26 (26 requested) and removed 29 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.71 2.89 Search for helices and strands: 0 residues in 0 chains, 3670 seeds are put forward Round 1: 225 peptides, 38 chains. Longest chain 11 peptides. Score 0.350 Round 2: 266 peptides, 38 chains. Longest chain 18 peptides. Score 0.436 Round 3: 269 peptides, 38 chains. Longest chain 18 peptides. Score 0.442 Round 4: 264 peptides, 35 chains. Longest chain 21 peptides. Score 0.459 Round 5: 260 peptides, 35 chains. Longest chain 17 peptides. Score 0.451 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 229, Estimated correctness of the model 0.0 % 1 chains (20 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2o5r-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11761 reflections ( 99.27 % complete ) and 7691 restraints for refining 3499 atoms. 6697 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2930 (Rfree = 0.000) for 3499 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2863 (Rfree = 0.000) for 3456 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2788 (Rfree = 0.000) for 3433 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.2757 (Rfree = 0.000) for 3407 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Writing output files ... TimeTaking 69.21