Sun 23 Dec 22:22:40 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-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o5r-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o5r-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o5r-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/2o5r-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o5r-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 22:22:49 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-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o5r-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 496 and 0 Target number of residues in the AU: 496 Target solvent content: 0.6654 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-3.2-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: 152 Cell parameters: 69.953 69.953 283.945 90.000 90.000 120.000 Input sequence file: 2o5r-3.2-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 3.200 Wilson plot Bfac: 88.77 14014 reflections ( 99.37 % complete ) and 0 restraints for refining 4236 atoms. Observations/parameters ratio is 0.83 ------------------------------------------------------ Starting model: R = 0.3406 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3434 (Rfree = 0.000) for 4236 atoms. Found 38 (38 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.75 2.92 Search for helices and strands: 0 residues in 0 chains, 4333 seeds are put forward Round 1: 226 peptides, 40 chains. Longest chain 18 peptides. Score 0.332 Round 2: 267 peptides, 33 chains. Longest chain 15 peptides. Score 0.482 Round 3: 304 peptides, 33 chains. Longest chain 26 peptides. Score 0.548 Round 4: 305 peptides, 35 chains. Longest chain 21 peptides. Score 0.534 Round 5: 309 peptides, 31 chains. Longest chain 22 peptides. Score 0.572 Taking the results from Round 5 Chains 34, Residues 278, Estimated correctness of the model 33.3 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 14014 reflections ( 99.37 % complete ) and 7506 restraints for refining 3509 atoms. 6337 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3185 (Rfree = 0.000) for 3509 atoms. Found 31 (31 requested) and removed 29 (15 requested) atoms. Cycle 2: After refmac, R = 0.3087 (Rfree = 0.000) for 3447 atoms. Found 31 (31 requested) and removed 26 (15 requested) atoms. Cycle 3: After refmac, R = 0.3045 (Rfree = 0.000) for 3406 atoms. Found 30 (30 requested) and removed 24 (15 requested) atoms. Cycle 4: After refmac, R = 0.2757 (Rfree = 0.000) for 3384 atoms. Found 25 (30 requested) and removed 22 (15 requested) atoms. Cycle 5: After refmac, R = 0.2684 (Rfree = 0.000) for 3361 atoms. Found 22 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.64 2.83 Search for helices and strands: 0 residues in 0 chains, 3542 seeds are put forward Round 1: 286 peptides, 34 chains. Longest chain 16 peptides. Score 0.509 Round 2: 321 peptides, 36 chains. Longest chain 22 peptides. Score 0.553 Round 3: 321 peptides, 33 chains. Longest chain 34 peptides. Score 0.576 Round 4: 313 peptides, 32 chains. Longest chain 31 peptides. Score 0.571 Round 5: 338 peptides, 32 chains. Longest chain 28 peptides. Score 0.610 Taking the results from Round 5 Chains 35, Residues 306, Estimated correctness of the model 43.7 % 3 chains (49 residues) have been docked in sequence ------------------------------------------------------ 14014 reflections ( 99.37 % complete ) and 6919 restraints for refining 3513 atoms. 5516 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2976 (Rfree = 0.000) for 3513 atoms. Found 31 (31 requested) and removed 29 (15 requested) atoms. Cycle 7: After refmac, R = 0.2950 (Rfree = 0.000) for 3475 atoms. Found 31 (31 requested) and removed 26 (15 requested) atoms. Cycle 8: After refmac, R = 0.2736 (Rfree = 0.000) for 3463 atoms. Found 14 (31 requested) and removed 24 (15 requested) atoms. Cycle 9: After refmac, R = 0.2696 (Rfree = 0.000) for 3439 atoms. Found 10 (30 requested) and removed 22 (15 requested) atoms. Cycle 10: After refmac, R = 0.2687 (Rfree = 0.000) for 3419 atoms. Found 8 (30 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.76 2.93 Search for helices and strands: 0 residues in 0 chains, 3575 seeds are put forward Round 1: 301 peptides, 36 chains. Longest chain 19 peptides. Score 0.519 Round 2: 330 peptides, 32 chains. Longest chain 28 peptides. Score 0.598 Round 3: 325 peptides, 33 chains. Longest chain 30 peptides. Score 0.583 Round 4: 321 peptides, 29 chains. Longest chain 48 peptides. Score 0.607 Round 5: 317 peptides, 32 chains. Longest chain 31 peptides. Score 0.578 Taking the results from Round 4 Chains 34, Residues 292, Estimated correctness of the model 42.9 % 4 chains (58 residues) have been docked in sequence ------------------------------------------------------ 14014 reflections ( 99.37 % complete ) and 6798 restraints for refining 3512 atoms. 5398 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2875 (Rfree = 0.000) for 3512 atoms. Found 31 (31 requested) and removed 29 (15 requested) atoms. Cycle 12: After refmac, R = 0.2659 (Rfree = 0.000) for 3490 atoms. Found 20 (31 requested) and removed 23 (15 requested) atoms. Cycle 13: After refmac, R = 0.2595 (Rfree = 0.000) for 3469 atoms. Found 16 (31 requested) and removed 24 (15 requested) atoms. Cycle 14: After refmac, R = 0.2676 (Rfree = 0.000) for 3440 atoms. Found 20 (31 requested) and removed 25 (15 requested) atoms. Cycle 15: After refmac, R = 0.2577 (Rfree = 0.000) for 3416 atoms. Found 19 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.66 2.85 Search for helices and strands: 0 residues in 0 chains, 3545 seeds are put forward Round 1: 287 peptides, 39 chains. Longest chain 21 peptides. Score 0.468 Round 2: 326 peptides, 37 chains. Longest chain 30 peptides. Score 0.554 Round 3: 315 peptides, 36 chains. Longest chain 26 peptides. Score 0.543 Round 4: 321 peptides, 34 chains. Longest chain 25 peptides. Score 0.569 Round 5: 341 peptides, 33 chains. Longest chain 32 peptides. Score 0.608 Taking the results from Round 5 Chains 34, Residues 308, Estimated correctness of the model 43.2 % 2 chains (48 residues) have been docked in sequence ------------------------------------------------------ 14014 reflections ( 99.37 % complete ) and 6867 restraints for refining 3513 atoms. 5463 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2901 (Rfree = 0.000) for 3513 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. Cycle 17: After refmac, R = 0.2758 (Rfree = 0.000) for 3477 atoms. Found 29 (31 requested) and removed 24 (15 requested) atoms. Cycle 18: After refmac, R = 0.2577 (Rfree = 0.000) for 3469 atoms. Found 11 (31 requested) and removed 17 (15 requested) atoms. Cycle 19: After refmac, R = 0.2653 (Rfree = 0.000) for 3447 atoms. Found 24 (31 requested) and removed 19 (15 requested) atoms. Cycle 20: After refmac, R = 0.2589 (Rfree = 0.000) for 3428 atoms. Found 15 (30 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 2.82 Search for helices and strands: 0 residues in 0 chains, 3564 seeds are put forward Round 1: 315 peptides, 45 chains. Longest chain 19 peptides. Score 0.469 Round 2: 312 peptides, 36 chains. Longest chain 25 peptides. Score 0.538 Round 3: 308 peptides, 35 chains. Longest chain 24 peptides. Score 0.539 Round 4: 304 peptides, 33 chains. Longest chain 30 peptides. Score 0.548 Round 5: 315 peptides, 37 chains. Longest chain 23 peptides. Score 0.535 Taking the results from Round 4 Chains 33, Residues 271, Estimated correctness of the model 26.3 % 3 chains (59 residues) have been docked in sequence ------------------------------------------------------ 14014 reflections ( 99.37 % complete ) and 7024 restraints for refining 3513 atoms. 5714 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2864 (Rfree = 0.000) for 3513 atoms. Found 31 (31 requested) and removed 25 (15 requested) atoms. Cycle 22: After refmac, R = 0.2745 (Rfree = 0.000) for 3501 atoms. Found 26 (31 requested) and removed 28 (15 requested) atoms. Cycle 23: After refmac, R = 0.2828 (Rfree = 0.000) for 3487 atoms. Found 31 (31 requested) and removed 40 (15 requested) atoms. Cycle 24: After refmac, R = 0.2605 (Rfree = 0.000) for 3456 atoms. Found 30 (31 requested) and removed 21 (15 requested) atoms. Cycle 25: After refmac, R = 0.2578 (Rfree = 0.000) for 3445 atoms. Found 18 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 2.80 Search for helices and strands: 0 residues in 0 chains, 3577 seeds are put forward Round 1: 300 peptides, 39 chains. Longest chain 26 peptides. Score 0.492 Round 2: 318 peptides, 35 chains. Longest chain 27 peptides. Score 0.556 Round 3: 331 peptides, 38 chains. Longest chain 31 peptides. Score 0.554 Round 4: 318 peptides, 38 chains. Longest chain 27 peptides. Score 0.532 Round 5: 306 peptides, 38 chains. Longest chain 22 peptides. Score 0.511 Taking the results from Round 2 Chains 37, Residues 283, Estimated correctness of the model 28.7 % 6 chains (75 residues) have been docked in sequence ------------------------------------------------------ 14014 reflections ( 99.37 % complete ) and 6741 restraints for refining 3513 atoms. 5346 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2774 (Rfree = 0.000) for 3513 atoms. Found 26 (31 requested) and removed 20 (15 requested) atoms. Cycle 27: After refmac, R = 0.2717 (Rfree = 0.000) for 3495 atoms. Found 31 (31 requested) and removed 23 (15 requested) atoms. Cycle 28: After refmac, R = 0.2644 (Rfree = 0.000) for 3489 atoms. Found 20 (31 requested) and removed 21 (15 requested) atoms. Cycle 29: After refmac, R = 0.2622 (Rfree = 0.000) for 3479 atoms. Found 17 (31 requested) and removed 18 (15 requested) atoms. Cycle 30: After refmac, R = 0.2462 (Rfree = 0.000) for 3473 atoms. Found 7 (31 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.60 2.80 Search for helices and strands: 0 residues in 0 chains, 3623 seeds are put forward Round 1: 269 peptides, 40 chains. Longest chain 19 peptides. Score 0.424 Round 2: 306 peptides, 37 chains. Longest chain 29 peptides. Score 0.519 Round 3: 307 peptides, 40 chains. Longest chain 20 peptides. Score 0.496 Round 4: 307 peptides, 38 chains. Longest chain 33 peptides. Score 0.513 Round 5: 305 peptides, 34 chains. Longest chain 28 peptides. Score 0.542 Taking the results from Round 5 Chains 35, Residues 271, Estimated correctness of the model 24.5 % 4 chains (60 residues) have been docked in sequence ------------------------------------------------------ 14014 reflections ( 99.37 % complete ) and 7036 restraints for refining 3512 atoms. 5738 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2837 (Rfree = 0.000) for 3512 atoms. Found 31 (31 requested) and removed 19 (15 requested) atoms. Cycle 32: After refmac, R = 0.2667 (Rfree = 0.000) for 3492 atoms. Found 21 (31 requested) and removed 17 (15 requested) atoms. Cycle 33: After refmac, R = 0.2699 (Rfree = 0.000) for 3476 atoms. Found 20 (31 requested) and removed 20 (15 requested) atoms. Cycle 34: After refmac, R = 0.2628 (Rfree = 0.000) for 3457 atoms. Found 31 (31 requested) and removed 16 (15 requested) atoms. Cycle 35: After refmac, R = 0.2590 (Rfree = 0.000) for 3464 atoms. Found 21 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 2.81 Search for helices and strands: 0 residues in 0 chains, 3623 seeds are put forward Round 1: 270 peptides, 36 chains. Longest chain 22 peptides. Score 0.461 Round 2: 324 peptides, 36 chains. Longest chain 31 peptides. Score 0.558 Round 3: 332 peptides, 35 chains. Longest chain 22 peptides. Score 0.579 Round 4: 312 peptides, 35 chains. Longest chain 21 peptides. Score 0.546 Round 5: 310 peptides, 30 chains. Longest chain 30 peptides. Score 0.582 Taking the results from Round 5 Chains 31, Residues 280, Estimated correctness of the model 36.1 % 4 chains (74 residues) have been docked in sequence ------------------------------------------------------ 14014 reflections ( 99.37 % complete ) and 6845 restraints for refining 3513 atoms. 5439 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2820 (Rfree = 0.000) for 3513 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. Cycle 37: After refmac, R = 0.2692 (Rfree = 0.000) for 3490 atoms. Found 20 (31 requested) and removed 20 (15 requested) atoms. Cycle 38: After refmac, R = 0.2883 (Rfree = 0.000) for 3479 atoms. Found 31 (31 requested) and removed 28 (15 requested) atoms. Cycle 39: After refmac, R = 0.2632 (Rfree = 0.000) for 3473 atoms. Found 25 (31 requested) and removed 20 (15 requested) atoms. Cycle 40: After refmac, R = 0.2581 (Rfree = 0.000) for 3461 atoms. Found 18 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 2.79 Search for helices and strands: 0 residues in 0 chains, 3636 seeds are put forward Round 1: 281 peptides, 41 chains. Longest chain 17 peptides. Score 0.439 Round 2: 308 peptides, 36 chains. Longest chain 30 peptides. Score 0.531 Round 3: 305 peptides, 33 chains. Longest chain 21 peptides. Score 0.550 Round 4: 310 peptides, 30 chains. Longest chain 32 peptides. Score 0.582 Round 5: 290 peptides, 35 chains. Longest chain 26 peptides. Score 0.507 Taking the results from Round 4 Chains 36, Residues 280, Estimated correctness of the model 36.1 % 5 chains (71 residues) have been docked in sequence ------------------------------------------------------ 14014 reflections ( 99.37 % complete ) and 6907 restraints for refining 3512 atoms. 5497 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2988 (Rfree = 0.000) for 3512 atoms. Found 31 (31 requested) and removed 30 (15 requested) atoms. Cycle 42: After refmac, R = 0.2782 (Rfree = 0.000) for 3475 atoms. Found 21 (31 requested) and removed 23 (15 requested) atoms. Cycle 43: After refmac, R = 0.2742 (Rfree = 0.000) for 3453 atoms. Found 29 (31 requested) and removed 23 (15 requested) atoms. Cycle 44: After refmac, R = 0.2644 (Rfree = 0.000) for 3449 atoms. Found 13 (31 requested) and removed 21 (15 requested) atoms. Cycle 45: After refmac, R = 0.2600 (Rfree = 0.000) for 3425 atoms. Found 9 (30 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 2.84 Search for helices and strands: 0 residues in 0 chains, 3560 seeds are put forward Round 1: 268 peptides, 46 chains. Longest chain 15 peptides. Score 0.367 Round 2: 299 peptides, 39 chains. Longest chain 26 peptides. Score 0.490 Round 3: 289 peptides, 41 chains. Longest chain 19 peptides. Score 0.454 Round 4: 301 peptides, 37 chains. Longest chain 32 peptides. Score 0.510 Round 5: 301 peptides, 36 chains. Longest chain 27 peptides. Score 0.519 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 38, Residues 265, Estimated correctness of the model 17.4 % 3 chains (47 residues) have been docked in sequence Sequence coverage is 17 % Consider running further cycles of model building using 2o5r-3_warpNtrace.pdb as input Building loops using Loopy2018 38 chains (265 residues) following loop building 3 chains (47 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14014 reflections ( 99.37 % complete ) and 7165 restraints for refining 3513 atoms. 5936 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2867 (Rfree = 0.000) for 3513 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2812 (Rfree = 0.000) for 3478 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2757 (Rfree = 0.000) for 3447 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.2701 (Rfree = 0.000) for 3419 atoms. TimeTaking 66.7