Sun 23 Dec 22:23:05 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 1zy9-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zy9-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zy9-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zy9-3.4-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/1zy9-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zy9-3.4-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 ============================================================ Sun 23 Dec 22:23:14 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/1zy9-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zy9-3.4-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 620 and 0 Target number of residues in the AU: 620 Target solvent content: 0.6116 Checking the provided sequence file Detected sequence length: 564 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 564 Adjusted target solvent content: 0.65 Input MTZ file: 1zy9-3.4-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: 20 Cell parameters: 121.755 160.844 88.238 90.000 90.000 90.000 Input sequence file: 1zy9-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 4512 target number of atoms Had to go as low as 0.75 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: 97.078 3.400 Wilson plot Bfac: 57.43 11785 reflections ( 96.06 % complete ) and 0 restraints for refining 5011 atoms. Observations/parameters ratio is 0.59 ------------------------------------------------------ Starting model: R = 0.3049 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2663 (Rfree = 0.000) for 5011 atoms. Found 37 (37 requested) and removed 55 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 2.59 Search for helices and strands: 0 residues in 0 chains, 5101 seeds are put forward Round 1: 333 peptides, 53 chains. Longest chain 17 peptides. Score 0.422 Round 2: 385 peptides, 51 chains. Longest chain 20 peptides. Score 0.526 Round 3: 395 peptides, 45 chains. Longest chain 19 peptides. Score 0.583 Round 4: 394 peptides, 45 chains. Longest chain 34 peptides. Score 0.582 Round 5: 395 peptides, 40 chains. Longest chain 33 peptides. Score 0.616 Taking the results from Round 5 Chains 45, Residues 355, Estimated correctness of the model 33.8 % 4 chains (57 residues) have been docked in sequence ------------------------------------------------------ 11785 reflections ( 96.06 % complete ) and 8347 restraints for refining 4103 atoms. 6763 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2658 (Rfree = 0.000) for 4103 atoms. Found 30 (30 requested) and removed 20 (15 requested) atoms. Cycle 2: After refmac, R = 0.2585 (Rfree = 0.000) for 4054 atoms. Found 31 (31 requested) and removed 18 (15 requested) atoms. Cycle 3: After refmac, R = 0.2501 (Rfree = 0.000) for 4047 atoms. Found 27 (30 requested) and removed 17 (15 requested) atoms. Cycle 4: After refmac, R = 0.2463 (Rfree = 0.000) for 4044 atoms. Found 18 (30 requested) and removed 19 (15 requested) atoms. Cycle 5: After refmac, R = 0.2504 (Rfree = 0.000) for 4021 atoms. Found 28 (30 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.15 2.56 Search for helices and strands: 0 residues in 0 chains, 4155 seeds are put forward Round 1: 370 peptides, 48 chains. Longest chain 19 peptides. Score 0.524 Round 2: 401 peptides, 42 chains. Longest chain 21 peptides. Score 0.612 Round 3: 401 peptides, 36 chains. Longest chain 39 peptides. Score 0.650 Round 4: 421 peptides, 38 chains. Longest chain 51 peptides. Score 0.663 Round 5: 410 peptides, 39 chains. Longest chain 27 peptides. Score 0.643 Taking the results from Round 4 Chains 42, Residues 383, Estimated correctness of the model 47.9 % 6 chains (112 residues) have been docked in sequence ------------------------------------------------------ 11785 reflections ( 96.06 % complete ) and 7568 restraints for refining 4103 atoms. 5614 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2858 (Rfree = 0.000) for 4103 atoms. Found 30 (30 requested) and removed 34 (15 requested) atoms. Cycle 7: After refmac, R = 0.2820 (Rfree = 0.000) for 4076 atoms. Found 23 (30 requested) and removed 22 (15 requested) atoms. Cycle 8: After refmac, R = 0.2825 (Rfree = 0.000) for 4064 atoms. Found 30 (30 requested) and removed 32 (15 requested) atoms. Cycle 9: After refmac, R = 0.2592 (Rfree = 0.000) for 4050 atoms. Found 21 (30 requested) and removed 21 (15 requested) atoms. Cycle 10: After refmac, R = 0.2570 (Rfree = 0.000) for 4039 atoms. Found 12 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.13 2.55 Search for helices and strands: 0 residues in 0 chains, 4137 seeds are put forward Round 1: 386 peptides, 47 chains. Longest chain 27 peptides. Score 0.556 Round 2: 404 peptides, 42 chains. Longest chain 34 peptides. Score 0.616 Round 3: 406 peptides, 40 chains. Longest chain 27 peptides. Score 0.631 Round 4: 414 peptides, 37 chains. Longest chain 46 peptides. Score 0.660 Round 5: 402 peptides, 39 chains. Longest chain 34 peptides. Score 0.632 Taking the results from Round 4 Chains 40, Residues 377, Estimated correctness of the model 47.0 % 3 chains (67 residues) have been docked in sequence ------------------------------------------------------ 11785 reflections ( 96.06 % complete ) and 8044 restraints for refining 4103 atoms. 6280 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2708 (Rfree = 0.000) for 4103 atoms. Found 30 (30 requested) and removed 32 (15 requested) atoms. Cycle 12: After refmac, R = 0.2652 (Rfree = 0.000) for 4077 atoms. Found 23 (30 requested) and removed 19 (15 requested) atoms. Cycle 13: After refmac, R = 0.2580 (Rfree = 0.000) for 4076 atoms. Found 14 (30 requested) and removed 16 (15 requested) atoms. Cycle 14: After refmac, R = 0.2569 (Rfree = 0.000) for 4069 atoms. Found 7 (30 requested) and removed 15 (15 requested) atoms. Cycle 15: After refmac, R = 0.2537 (Rfree = 0.000) for 4058 atoms. Found 5 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 2.58 Search for helices and strands: 0 residues in 0 chains, 4163 seeds are put forward Round 1: 384 peptides, 47 chains. Longest chain 22 peptides. Score 0.553 Round 2: 411 peptides, 36 chains. Longest chain 40 peptides. Score 0.662 Round 3: 403 peptides, 44 chains. Longest chain 28 peptides. Score 0.601 Round 4: 415 peptides, 40 chains. Longest chain 31 peptides. Score 0.643 Round 5: 406 peptides, 40 chains. Longest chain 36 peptides. Score 0.631 Taking the results from Round 2 Chains 41, Residues 375, Estimated correctness of the model 47.6 % 5 chains (83 residues) have been docked in sequence ------------------------------------------------------ 11785 reflections ( 96.06 % complete ) and 7834 restraints for refining 4103 atoms. 6023 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2770 (Rfree = 0.000) for 4103 atoms. Found 30 (30 requested) and removed 25 (15 requested) atoms. Cycle 17: After refmac, R = 0.2634 (Rfree = 0.000) for 4093 atoms. Found 17 (31 requested) and removed 17 (15 requested) atoms. Cycle 18: After refmac, R = 0.2527 (Rfree = 0.000) for 4084 atoms. Found 18 (30 requested) and removed 15 (15 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2470 (Rfree = 0.000) for 4083 atoms. Found 6 (30 requested) and removed 16 (15 requested) atoms. Cycle 20: After refmac, R = 0.2422 (Rfree = 0.000) for 4067 atoms. Found 15 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 2.56 Search for helices and strands: 0 residues in 0 chains, 4162 seeds are put forward Round 1: 370 peptides, 45 chains. Longest chain 30 peptides. Score 0.546 Round 2: 394 peptides, 45 chains. Longest chain 27 peptides. Score 0.582 Round 3: 407 peptides, 42 chains. Longest chain 27 peptides. Score 0.620 Round 4: 405 peptides, 41 chains. Longest chain 29 peptides. Score 0.624 Round 5: 389 peptides, 40 chains. Longest chain 35 peptides. Score 0.608 Taking the results from Round 4 Chains 43, Residues 364, Estimated correctness of the model 36.3 % 7 chains (87 residues) have been docked in sequence ------------------------------------------------------ 11785 reflections ( 96.06 % complete ) and 8011 restraints for refining 4103 atoms. 6259 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2772 (Rfree = 0.000) for 4103 atoms. Found 30 (30 requested) and removed 28 (15 requested) atoms. Cycle 22: After refmac, R = 0.2594 (Rfree = 0.000) for 4088 atoms. Found 29 (30 requested) and removed 21 (15 requested) atoms. Cycle 23: After refmac, R = 0.2501 (Rfree = 0.000) for 4086 atoms. Found 25 (30 requested) and removed 17 (15 requested) atoms. Cycle 24: After refmac, R = 0.2445 (Rfree = 0.000) for 4088 atoms. Found 15 (30 requested) and removed 16 (15 requested) atoms. Cycle 25: After refmac, R = 0.2406 (Rfree = 0.000) for 4085 atoms. Found 7 (30 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 2.54 Search for helices and strands: 0 residues in 0 chains, 4198 seeds are put forward Round 1: 378 peptides, 50 chains. Longest chain 21 peptides. Score 0.522 Round 2: 395 peptides, 40 chains. Longest chain 28 peptides. Score 0.616 Round 3: 405 peptides, 38 chains. Longest chain 36 peptides. Score 0.642 Round 4: 407 peptides, 39 chains. Longest chain 29 peptides. Score 0.639 Round 5: 414 peptides, 39 chains. Longest chain 27 peptides. Score 0.648 Taking the results from Round 5 Chains 43, Residues 375, Estimated correctness of the model 43.6 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 11785 reflections ( 96.06 % complete ) and 8286 restraints for refining 4103 atoms. 6698 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2714 (Rfree = 0.000) for 4103 atoms. Found 30 (30 requested) and removed 17 (15 requested) atoms. Cycle 27: After refmac, R = 0.2648 (Rfree = 0.000) for 4107 atoms. Found 16 (31 requested) and removed 16 (15 requested) atoms. Cycle 28: After refmac, R = 0.2568 (Rfree = 0.000) for 4104 atoms. Found 6 (31 requested) and removed 15 (15 requested) atoms. Cycle 29: After refmac, R = 0.2528 (Rfree = 0.000) for 4094 atoms. Found 6 (30 requested) and removed 15 (15 requested) atoms. Cycle 30: After refmac, R = 0.2512 (Rfree = 0.000) for 4083 atoms. Found 7 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.19 2.60 Search for helices and strands: 0 residues in 0 chains, 4176 seeds are put forward Round 1: 382 peptides, 49 chains. Longest chain 30 peptides. Score 0.536 Round 2: 405 peptides, 42 chains. Longest chain 26 peptides. Score 0.617 Round 3: 382 peptides, 37 chains. Longest chain 35 peptides. Score 0.618 Round 4: 397 peptides, 40 chains. Longest chain 28 peptides. Score 0.619 Round 5: 402 peptides, 39 chains. Longest chain 28 peptides. Score 0.632 Taking the results from Round 5 Chains 42, Residues 363, Estimated correctness of the model 38.8 % 4 chains (66 residues) have been docked in sequence ------------------------------------------------------ 11785 reflections ( 96.06 % complete ) and 8245 restraints for refining 4103 atoms. 6571 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2808 (Rfree = 0.000) for 4103 atoms. Found 30 (30 requested) and removed 23 (15 requested) atoms. Cycle 32: After refmac, R = 0.2656 (Rfree = 0.000) for 4088 atoms. Found 30 (31 requested) and removed 19 (15 requested) atoms. Cycle 33: After refmac, R = 0.2599 (Rfree = 0.000) for 4080 atoms. Found 17 (30 requested) and removed 16 (15 requested) atoms. Cycle 34: After refmac, R = 0.2537 (Rfree = 0.000) for 4069 atoms. Found 19 (30 requested) and removed 22 (15 requested) atoms. Cycle 35: After refmac, R = 0.2522 (Rfree = 0.000) for 4055 atoms. Found 13 (30 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.13 2.55 Search for helices and strands: 0 residues in 0 chains, 4169 seeds are put forward Round 1: 384 peptides, 45 chains. Longest chain 23 peptides. Score 0.567 Round 2: 405 peptides, 41 chains. Longest chain 31 peptides. Score 0.624 Round 3: 417 peptides, 38 chains. Longest chain 26 peptides. Score 0.658 Round 4: 397 peptides, 38 chains. Longest chain 25 peptides. Score 0.632 Round 5: 407 peptides, 40 chains. Longest chain 34 peptides. Score 0.633 Taking the results from Round 3 Chains 39, Residues 379, Estimated correctness of the model 46.5 % 3 chains (52 residues) have been docked in sequence ------------------------------------------------------ 11785 reflections ( 96.06 % complete ) and 8176 restraints for refining 4103 atoms. 6462 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2673 (Rfree = 0.000) for 4103 atoms. Found 30 (30 requested) and removed 22 (15 requested) atoms. Cycle 37: After refmac, R = 0.2528 (Rfree = 0.000) for 4091 atoms. Found 16 (31 requested) and removed 21 (15 requested) atoms. Cycle 38: After refmac, R = 0.2540 (Rfree = 0.000) for 4077 atoms. Found 18 (30 requested) and removed 21 (15 requested) atoms. Cycle 39: After refmac, R = 0.2467 (Rfree = 0.000) for 4072 atoms. Found 16 (30 requested) and removed 16 (15 requested) atoms. Cycle 40: After refmac, R = 0.2515 (Rfree = 0.000) for 4066 atoms. Found 14 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 2.56 Search for helices and strands: 0 residues in 0 chains, 4163 seeds are put forward Round 1: 367 peptides, 42 chains. Longest chain 21 peptides. Score 0.562 Round 2: 403 peptides, 35 chains. Longest chain 30 peptides. Score 0.658 Round 3: 387 peptides, 37 chains. Longest chain 35 peptides. Score 0.625 Round 4: 403 peptides, 34 chains. Longest chain 38 peptides. Score 0.664 Round 5: 406 peptides, 38 chains. Longest chain 29 peptides. Score 0.644 Taking the results from Round 4 Chains 36, Residues 369, Estimated correctness of the model 48.2 % 3 chains (61 residues) have been docked in sequence ------------------------------------------------------ 11785 reflections ( 96.06 % complete ) and 8131 restraints for refining 4102 atoms. 6411 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2537 (Rfree = 0.000) for 4102 atoms. Found 30 (30 requested) and removed 30 (15 requested) atoms. Cycle 42: After refmac, R = 0.2409 (Rfree = 0.000) for 4083 atoms. Found 14 (30 requested) and removed 19 (15 requested) atoms. Cycle 43: After refmac, R = 0.2319 (Rfree = 0.000) for 4065 atoms. Found 16 (30 requested) and removed 20 (15 requested) atoms. Cycle 44: After refmac, R = 0.2311 (Rfree = 0.000) for 4054 atoms. Found 16 (30 requested) and removed 15 (15 requested) atoms. Cycle 45: After refmac, R = 0.2274 (Rfree = 0.000) for 4049 atoms. Found 11 (30 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 2.52 Search for helices and strands: 0 residues in 0 chains, 4153 seeds are put forward Round 1: 351 peptides, 41 chains. Longest chain 27 peptides. Score 0.545 Round 2: 389 peptides, 39 chains. Longest chain 44 peptides. Score 0.615 Round 3: 403 peptides, 38 chains. Longest chain 27 peptides. Score 0.640 Round 4: 398 peptides, 42 chains. Longest chain 25 peptides. Score 0.608 Round 5: 385 peptides, 40 chains. Longest chain 26 peptides. Score 0.603 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 365, Estimated correctness of the model 41.2 % 4 chains (61 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 1zy9-3_warpNtrace.pdb as input Building loops using Loopy2018 40 chains (365 residues) following loop building 4 chains (61 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11785 reflections ( 96.06 % complete ) and 7987 restraints for refining 4101 atoms. 6266 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2552 (Rfree = 0.000) for 4101 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2431 (Rfree = 0.000) for 4071 atoms. Found 0 (30 requested) and removed 7 (15 requested) atoms. Cycle 48: After refmac, R = 0.2390 (Rfree = 0.000) for 4058 atoms. Found 0 (30 requested) and removed 3 (15 requested) atoms. Cycle 49: After refmac, R = 0.2339 (Rfree = 0.000) for 4052 atoms. TimeTaking 67.15