Sun 23 Dec 22:22:56 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 2ppv-2.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ppv-2.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ppv-2.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ppv-2.5-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/2ppv-2.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ppv-2.5-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 22:23:06 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/2ppv-2.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ppv-2.5-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 397 and 0 Target number of residues in the AU: 397 Target solvent content: 0.5803 Checking the provided sequence file Detected sequence length: 332 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 332 Adjusted target solvent content: 0.65 Input MTZ file: 2ppv-2.5-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: 20 Cell parameters: 133.390 136.620 56.180 90.000 90.000 90.000 Input sequence file: 2ppv-2.5-parrot-hancs.fasta_lf Building free atoms model in initial map for 2656 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.185 2.504 Wilson plot Bfac: 44.99 17636 reflections ( 97.29 % complete ) and 0 restraints for refining 2950 atoms. Observations/parameters ratio is 1.49 ------------------------------------------------------ Starting model: R = 0.3325 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3014 (Rfree = 0.000) for 2950 atoms. Found 41 (53 requested) and removed 30 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.78 2.26 Round 1: 198 peptides, 35 chains. Longest chain 18 peptides. Score 0.375 Round 2: 214 peptides, 27 chains. Longest chain 19 peptides. Score 0.528 Round 3: 225 peptides, 27 chains. Longest chain 29 peptides. Score 0.557 Round 4: 246 peptides, 26 chains. Longest chain 24 peptides. Score 0.619 Round 5: 250 peptides, 25 chains. Longest chain 28 peptides. Score 0.639 Taking the results from Round 5 Chains 27, Residues 225, Estimated correctness of the model 77.5 % 2 chains (34 residues) have been docked in sequence ------------------------------------------------------ 17636 reflections ( 97.29 % complete ) and 4780 restraints for refining 2488 atoms. 3782 conditional restraints added. Observations/parameters ratio is 1.77 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3331 (Rfree = 0.000) for 2488 atoms. Found 44 (44 requested) and removed 31 (22 requested) atoms. Cycle 2: After refmac, R = 0.3168 (Rfree = 0.000) for 2477 atoms. Found 39 (45 requested) and removed 34 (22 requested) atoms. Cycle 3: After refmac, R = 0.3104 (Rfree = 0.000) for 2438 atoms. Found 36 (44 requested) and removed 27 (22 requested) atoms. Cycle 4: After refmac, R = 0.3025 (Rfree = 0.000) for 2407 atoms. Found 41 (44 requested) and removed 28 (22 requested) atoms. Cycle 5: After refmac, R = 0.2970 (Rfree = 0.000) for 2403 atoms. Found 33 (43 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.83 2.30 Round 1: 221 peptides, 27 chains. Longest chain 23 peptides. Score 0.547 Round 2: 239 peptides, 25 chains. Longest chain 30 peptides. Score 0.614 Round 3: 239 peptides, 25 chains. Longest chain 30 peptides. Score 0.614 Round 4: 250 peptides, 25 chains. Longest chain 40 peptides. Score 0.639 Round 5: 238 peptides, 22 chains. Longest chain 28 peptides. Score 0.644 Taking the results from Round 5 Chains 25, Residues 216, Estimated correctness of the model 78.1 % 3 chains (56 residues) have been docked in sequence ------------------------------------------------------ 17636 reflections ( 97.29 % complete ) and 4699 restraints for refining 2488 atoms. 3648 conditional restraints added. Observations/parameters ratio is 1.77 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3262 (Rfree = 0.000) for 2488 atoms. Found 44 (44 requested) and removed 36 (22 requested) atoms. Cycle 7: After refmac, R = 0.2974 (Rfree = 0.000) for 2487 atoms. Found 22 (45 requested) and removed 31 (22 requested) atoms. Cycle 8: After refmac, R = 0.2888 (Rfree = 0.000) for 2465 atoms. Found 19 (44 requested) and removed 23 (22 requested) atoms. Cycle 9: After refmac, R = 0.2851 (Rfree = 0.000) for 2455 atoms. Found 11 (44 requested) and removed 24 (22 requested) atoms. Cycle 10: After refmac, R = 0.2782 (Rfree = 0.000) for 2428 atoms. Found 10 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.72 2.21 Round 1: 221 peptides, 27 chains. Longest chain 27 peptides. Score 0.547 Round 2: 242 peptides, 22 chains. Longest chain 28 peptides. Score 0.653 Round 3: 248 peptides, 23 chains. Longest chain 29 peptides. Score 0.655 Round 4: 243 peptides, 24 chains. Longest chain 31 peptides. Score 0.634 Round 5: 246 peptides, 25 chains. Longest chain 28 peptides. Score 0.630 Taking the results from Round 3 Chains 30, Residues 225, Estimated correctness of the model 79.3 % 4 chains (63 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 17636 reflections ( 97.29 % complete ) and 4535 restraints for refining 2465 atoms. 3431 conditional restraints added. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3006 (Rfree = 0.000) for 2465 atoms. Found 44 (44 requested) and removed 28 (22 requested) atoms. Cycle 12: After refmac, R = 0.2807 (Rfree = 0.000) for 2472 atoms. Found 31 (44 requested) and removed 22 (22 requested) atoms. Cycle 13: After refmac, R = 0.2774 (Rfree = 0.000) for 2471 atoms. Found 20 (44 requested) and removed 22 (22 requested) atoms. Cycle 14: After refmac, R = 0.2658 (Rfree = 0.000) for 2459 atoms. Found 14 (44 requested) and removed 22 (22 requested) atoms. Cycle 15: After refmac, R = 0.2682 (Rfree = 0.000) for 2435 atoms. Found 24 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.69 2.19 Round 1: 234 peptides, 27 chains. Longest chain 27 peptides. Score 0.580 Round 2: 240 peptides, 24 chains. Longest chain 27 peptides. Score 0.627 Round 3: 248 peptides, 25 chains. Longest chain 28 peptides. Score 0.634 Round 4: 244 peptides, 27 chains. Longest chain 24 peptides. Score 0.604 Round 5: 236 peptides, 27 chains. Longest chain 23 peptides. Score 0.585 Taking the results from Round 3 Chains 29, Residues 223, Estimated correctness of the model 76.9 % 2 chains (34 residues) have been docked in sequence ------------------------------------------------------ 17636 reflections ( 97.29 % complete ) and 4789 restraints for refining 2486 atoms. 3796 conditional restraints added. Observations/parameters ratio is 1.77 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3001 (Rfree = 0.000) for 2486 atoms. Found 44 (44 requested) and removed 27 (22 requested) atoms. Cycle 17: After refmac, R = 0.2918 (Rfree = 0.000) for 2493 atoms. Found 42 (45 requested) and removed 24 (22 requested) atoms. Cycle 18: After refmac, R = 0.2786 (Rfree = 0.000) for 2491 atoms. Found 40 (45 requested) and removed 22 (22 requested) atoms. Cycle 19: After refmac, R = 0.2714 (Rfree = 0.000) for 2500 atoms. Found 19 (45 requested) and removed 22 (22 requested) atoms. Cycle 20: After refmac, R = 0.2591 (Rfree = 0.000) for 2484 atoms. Found 12 (45 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.67 2.17 Round 1: 213 peptides, 22 chains. Longest chain 27 peptides. Score 0.586 Round 2: 226 peptides, 23 chains. Longest chain 28 peptides. Score 0.606 Round 3: 234 peptides, 22 chains. Longest chain 40 peptides. Score 0.635 Round 4: 235 peptides, 23 chains. Longest chain 28 peptides. Score 0.626 Round 5: 238 peptides, 20 chains. Longest chain 36 peptides. Score 0.665 Taking the results from Round 5 Chains 26, Residues 218, Estimated correctness of the model 80.4 % 5 chains (67 residues) have been docked in sequence ------------------------------------------------------ 17636 reflections ( 97.29 % complete ) and 4593 restraints for refining 2488 atoms. 3500 conditional restraints added. Observations/parameters ratio is 1.77 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3073 (Rfree = 0.000) for 2488 atoms. Found 44 (44 requested) and removed 33 (22 requested) atoms. Cycle 22: After refmac, R = 0.2818 (Rfree = 0.000) for 2487 atoms. Found 33 (45 requested) and removed 27 (22 requested) atoms. Cycle 23: After refmac, R = 0.2782 (Rfree = 0.000) for 2476 atoms. Found 26 (45 requested) and removed 25 (22 requested) atoms. Cycle 24: After refmac, R = 0.2735 (Rfree = 0.000) for 2465 atoms. Found 21 (44 requested) and removed 26 (22 requested) atoms. Cycle 25: After refmac, R = 0.2727 (Rfree = 0.000) for 2446 atoms. Found 29 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.68 2.18 Round 1: 225 peptides, 26 chains. Longest chain 29 peptides. Score 0.569 Round 2: 243 peptides, 25 chains. Longest chain 22 peptides. Score 0.623 Round 3: 251 peptides, 21 chains. Longest chain 33 peptides. Score 0.681 Round 4: 256 peptides, 23 chains. Longest chain 29 peptides. Score 0.672 Round 5: 257 peptides, 26 chains. Longest chain 30 peptides. Score 0.644 Taking the results from Round 3 Chains 26, Residues 230, Estimated correctness of the model 82.1 % 5 chains (71 residues) have been docked in sequence ------------------------------------------------------ 17636 reflections ( 97.29 % complete ) and 4472 restraints for refining 2488 atoms. 3302 conditional restraints added. Observations/parameters ratio is 1.77 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2922 (Rfree = 0.000) for 2488 atoms. Found 40 (44 requested) and removed 31 (22 requested) atoms. Cycle 27: After refmac, R = 0.2705 (Rfree = 0.000) for 2481 atoms. Found 16 (45 requested) and removed 22 (22 requested) atoms. Cycle 28: After refmac, R = 0.2659 (Rfree = 0.000) for 2469 atoms. Found 9 (44 requested) and removed 23 (22 requested) atoms. Cycle 29: After refmac, R = 0.2595 (Rfree = 0.000) for 2451 atoms. Found 6 (44 requested) and removed 22 (22 requested) atoms. Cycle 30: After refmac, R = 0.2609 (Rfree = 0.000) for 2431 atoms. Found 11 (43 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.73 2.22 Round 1: 234 peptides, 29 chains. Longest chain 20 peptides. Score 0.557 Round 2: 250 peptides, 23 chains. Longest chain 25 peptides. Score 0.659 Round 3: 264 peptides, 24 chains. Longest chain 25 peptides. Score 0.678 Round 4: 259 peptides, 22 chains. Longest chain 43 peptides. Score 0.687 Round 5: 263 peptides, 27 chains. Longest chain 43 peptides. Score 0.647 Taking the results from Round 4 Chains 24, Residues 237, Estimated correctness of the model 82.7 % 4 chains (81 residues) have been docked in sequence ------------------------------------------------------ 17636 reflections ( 97.29 % complete ) and 4269 restraints for refining 2488 atoms. 3001 conditional restraints added. Observations/parameters ratio is 1.77 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3040 (Rfree = 0.000) for 2488 atoms. Found 35 (44 requested) and removed 34 (22 requested) atoms. Cycle 32: After refmac, R = 0.2787 (Rfree = 0.000) for 2482 atoms. Found 17 (44 requested) and removed 24 (22 requested) atoms. Cycle 33: After refmac, R = 0.2728 (Rfree = 0.000) for 2465 atoms. Found 17 (44 requested) and removed 22 (22 requested) atoms. Cycle 34: After refmac, R = 0.2616 (Rfree = 0.000) for 2449 atoms. Found 14 (44 requested) and removed 22 (22 requested) atoms. Cycle 35: After refmac, R = 0.2578 (Rfree = 0.000) for 2437 atoms. Found 10 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.67 2.17 Round 1: 235 peptides, 28 chains. Longest chain 24 peptides. Score 0.571 Round 2: 251 peptides, 21 chains. Longest chain 27 peptides. Score 0.681 Round 3: 250 peptides, 26 chains. Longest chain 22 peptides. Score 0.628 Round 4: 251 peptides, 21 chains. Longest chain 28 peptides. Score 0.681 Round 5: 236 peptides, 24 chains. Longest chain 24 peptides. Score 0.618 Taking the results from Round 4 Chains 21, Residues 230, Estimated correctness of the model 82.1 % 4 chains (82 residues) have been docked in sequence ------------------------------------------------------ 17636 reflections ( 97.29 % complete ) and 4324 restraints for refining 2486 atoms. 3092 conditional restraints added. Observations/parameters ratio is 1.77 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3088 (Rfree = 0.000) for 2486 atoms. Found 40 (44 requested) and removed 31 (22 requested) atoms. Cycle 37: After refmac, R = 0.2912 (Rfree = 0.000) for 2480 atoms. Found 25 (45 requested) and removed 28 (22 requested) atoms. Cycle 38: After refmac, R = 0.2854 (Rfree = 0.000) for 2463 atoms. Found 32 (44 requested) and removed 25 (22 requested) atoms. Cycle 39: After refmac, R = 0.2791 (Rfree = 0.000) for 2465 atoms. Found 17 (44 requested) and removed 22 (22 requested) atoms. Cycle 40: After refmac, R = 0.2756 (Rfree = 0.000) for 2455 atoms. Found 16 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.68 2.18 Round 1: 231 peptides, 23 chains. Longest chain 21 peptides. Score 0.617 Round 2: 240 peptides, 20 chains. Longest chain 28 peptides. Score 0.669 Round 3: 243 peptides, 24 chains. Longest chain 24 peptides. Score 0.634 Round 4: 245 peptides, 22 chains. Longest chain 28 peptides. Score 0.659 Round 5: 247 peptides, 20 chains. Longest chain 33 peptides. Score 0.683 Taking the results from Round 5 Chains 23, Residues 227, Estimated correctness of the model 82.3 % 5 chains (59 residues) have been docked in sequence ------------------------------------------------------ 17636 reflections ( 97.29 % complete ) and 4623 restraints for refining 2486 atoms. 3537 conditional restraints added. Observations/parameters ratio is 1.77 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3014 (Rfree = 0.000) for 2486 atoms. Found 28 (44 requested) and removed 25 (22 requested) atoms. Cycle 42: After refmac, R = 0.2778 (Rfree = 0.000) for 2476 atoms. Found 13 (44 requested) and removed 24 (22 requested) atoms. Cycle 43: After refmac, R = 0.2792 (Rfree = 0.000) for 2460 atoms. Found 18 (44 requested) and removed 22 (22 requested) atoms. Cycle 44: After refmac, R = 0.2629 (Rfree = 0.000) for 2453 atoms. Found 15 (44 requested) and removed 22 (22 requested) atoms. Cycle 45: After refmac, R = 0.2680 (Rfree = 0.000) for 2439 atoms. Found 16 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.66 2.16 Round 1: 226 peptides, 24 chains. Longest chain 25 peptides. Score 0.594 Round 2: 240 peptides, 18 chains. Longest chain 31 peptides. Score 0.689 Round 3: 243 peptides, 19 chains. Longest chain 49 peptides. Score 0.685 Round 4: 215 peptides, 20 chains. Longest chain 21 peptides. Score 0.614 Round 5: 232 peptides, 22 chains. Longest chain 23 peptides. Score 0.630 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 222, Estimated correctness of the model 82.9 % 6 chains (120 residues) have been docked in sequence Sequence coverage is 53 % Consider running further cycles of model building using 2ppv-2_warpNtrace.pdb as input Building loops using Loopy2018 23 chains (222 residues) following loop building 6 chains (120 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17636 reflections ( 97.29 % complete ) and 4043 restraints for refining 2488 atoms. 2707 conditional restraints added. Observations/parameters ratio is 1.77 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2749 (Rfree = 0.000) for 2488 atoms. Found 0 (44 requested) and removed 18 (22 requested) atoms. Cycle 47: After refmac, R = 0.2594 (Rfree = 0.000) for 2457 atoms. Found 0 (44 requested) and removed 7 (22 requested) atoms. Cycle 48: After refmac, R = 0.2546 (Rfree = 0.000) for 2445 atoms. Found 0 (44 requested) and removed 6 (22 requested) atoms. Cycle 49: After refmac, R = 0.2498 (Rfree = 0.000) for 2438 atoms. TimeTaking 54.65