Sun 23 Dec 22:22:43 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 2o7t-2.1-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o7t-2.1-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o7t-2.1-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o7t-2.1-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/2o7t-2.1-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o7t-2.1-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 22:22:53 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/2o7t-2.1-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o7t-2.1-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 168 and 0 Target number of residues in the AU: 168 Target solvent content: 0.5372 Checking the provided sequence file Detected sequence length: 199 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 199 Adjusted target solvent content: 0.45 Input MTZ file: 2o7t-2.1-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: 154 Cell parameters: 51.232 51.232 129.642 90.000 90.000 120.000 Input sequence file: 2o7t-2.1-parrot-hancs.fasta_lf Building free atoms model in initial map for 1592 target number of atoms Had to go as low as 0.55 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 1 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: 26.172 2.101 Wilson plot Bfac: 31.94 12083 reflections ( 99.83 % complete ) and 0 restraints for refining 1790 atoms. Observations/parameters ratio is 1.69 ------------------------------------------------------ Starting model: R = 0.3871 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3455 (Rfree = 0.000) for 1790 atoms. Found 14 (53 requested) and removed 44 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.60 2.78 Round 1: 71 peptides, 15 chains. Longest chain 8 peptides. Score 0.272 Round 2: 87 peptides, 13 chains. Longest chain 20 peptides. Score 0.477 Round 3: 94 peptides, 14 chains. Longest chain 21 peptides. Score 0.496 Round 4: 102 peptides, 13 chains. Longest chain 21 peptides. Score 0.580 Round 5: 102 peptides, 14 chains. Longest chain 20 peptides. Score 0.551 Taking the results from Round 4 Chains 13, Residues 89, Estimated correctness of the model 83.0 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.83 % complete ) and 3145 restraints for refining 1530 atoms. 2720 conditional restraints added. Observations/parameters ratio is 1.97 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3788 (Rfree = 0.000) for 1530 atoms. Found 19 (45 requested) and removed 25 (22 requested) atoms. Cycle 2: After refmac, R = 0.3727 (Rfree = 0.000) for 1504 atoms. Found 20 (45 requested) and removed 23 (22 requested) atoms. Cycle 3: After refmac, R = 0.3626 (Rfree = 0.000) for 1494 atoms. Found 24 (44 requested) and removed 23 (22 requested) atoms. Cycle 4: After refmac, R = 0.3592 (Rfree = 0.000) for 1488 atoms. Found 18 (44 requested) and removed 22 (22 requested) atoms. Cycle 5: After refmac, R = 0.3488 (Rfree = 0.000) for 1480 atoms. Found 17 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.33 2.49 Round 1: 88 peptides, 11 chains. Longest chain 21 peptides. Score 0.548 Round 2: 98 peptides, 11 chains. Longest chain 21 peptides. Score 0.612 Round 3: 106 peptides, 12 chains. Longest chain 21 peptides. Score 0.632 Round 4: 108 peptides, 11 chains. Longest chain 20 peptides. Score 0.668 Round 5: 109 peptides, 13 chains. Longest chain 20 peptides. Score 0.623 Taking the results from Round 4 Chains 11, Residues 97, Estimated correctness of the model 89.0 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 12083 reflections ( 99.83 % complete ) and 2882 restraints for refining 1467 atoms. 2375 conditional restraints added. Observations/parameters ratio is 2.06 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3587 (Rfree = 0.000) for 1467 atoms. Found 28 (43 requested) and removed 25 (21 requested) atoms. Cycle 7: After refmac, R = 0.3400 (Rfree = 0.000) for 1469 atoms. Found 18 (43 requested) and removed 21 (21 requested) atoms. Cycle 8: After refmac, R = 0.3309 (Rfree = 0.000) for 1463 atoms. Found 17 (43 requested) and removed 21 (21 requested) atoms. Cycle 9: After refmac, R = 0.3236 (Rfree = 0.000) for 1455 atoms. Found 13 (43 requested) and removed 21 (21 requested) atoms. Cycle 10: After refmac, R = 0.3198 (Rfree = 0.000) for 1441 atoms. Found 20 (42 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.38 2.54 Round 1: 115 peptides, 13 chains. Longest chain 20 peptides. Score 0.656 Round 2: 119 peptides, 11 chains. Longest chain 22 peptides. Score 0.722 Round 3: 124 peptides, 9 chains. Longest chain 31 peptides. Score 0.782 Round 4: 119 peptides, 11 chains. Longest chain 22 peptides. Score 0.722 Round 5: 129 peptides, 11 chains. Longest chain 21 peptides. Score 0.763 Taking the results from Round 3 Chains 9, Residues 115, Estimated correctness of the model 94.9 % 3 chains (70 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 76 A and 85 A 8 chains (123 residues) following loop building 2 chains (78 residues) in sequence following loop building ------------------------------------------------------ 12083 reflections ( 99.83 % complete ) and 2342 restraints for refining 1516 atoms. 1546 conditional restraints added. Observations/parameters ratio is 1.99 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3349 (Rfree = 0.000) for 1516 atoms. Found 39 (45 requested) and removed 24 (22 requested) atoms. Cycle 12: After refmac, R = 0.3132 (Rfree = 0.000) for 1525 atoms. Found 19 (44 requested) and removed 23 (22 requested) atoms. Cycle 13: After refmac, R = 0.3074 (Rfree = 0.000) for 1514 atoms. Found 12 (43 requested) and removed 22 (22 requested) atoms. Cycle 14: After refmac, R = 0.2992 (Rfree = 0.000) for 1500 atoms. Found 14 (41 requested) and removed 22 (22 requested) atoms. Cycle 15: After refmac, R = 0.2937 (Rfree = 0.000) for 1490 atoms. Found 9 (40 requested) and removed 5 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.31 2.47 Round 1: 129 peptides, 10 chains. Longest chain 27 peptides. Score 0.782 Round 2: 137 peptides, 10 chains. Longest chain 36 peptides. Score 0.808 Round 3: 137 peptides, 9 chains. Longest chain 55 peptides. Score 0.824 Round 4: 139 peptides, 11 chains. Longest chain 52 peptides. Score 0.799 Round 5: 141 peptides, 14 chains. Longest chain 27 peptides. Score 0.754 Taking the results from Round 3 Chains 9, Residues 128, Estimated correctness of the model 96.5 % 2 chains (72 residues) have been docked in sequence Building loops using Loopy2018 9 chains (128 residues) following loop building 2 chains (72 residues) in sequence following loop building ------------------------------------------------------ 12083 reflections ( 99.83 % complete ) and 2398 restraints for refining 1521 atoms. 1613 conditional restraints added. Observations/parameters ratio is 1.99 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3144 (Rfree = 0.000) for 1521 atoms. Found 17 (40 requested) and removed 25 (22 requested) atoms. Cycle 17: After refmac, R = 0.3036 (Rfree = 0.000) for 1506 atoms. Found 11 (40 requested) and removed 22 (22 requested) atoms. Cycle 18: After refmac, R = 0.2943 (Rfree = 0.000) for 1492 atoms. Found 5 (38 requested) and removed 17 (22 requested) atoms. Cycle 19: After refmac, R = 0.2918 (Rfree = 0.000) for 1476 atoms. Found 15 (37 requested) and removed 6 (22 requested) atoms. Cycle 20: After refmac, R = 0.3283 (Rfree = 0.000) for 1480 atoms. Found 20 (37 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.34 2.50 Round 1: 133 peptides, 10 chains. Longest chain 29 peptides. Score 0.795 Round 2: 141 peptides, 7 chains. Longest chain 62 peptides. Score 0.863 Round 3: 140 peptides, 10 chains. Longest chain 29 peptides. Score 0.818 Round 4: 138 peptides, 10 chains. Longest chain 39 peptides. Score 0.812 Round 5: 138 peptides, 9 chains. Longest chain 47 peptides. Score 0.827 Taking the results from Round 2 Chains 7, Residues 134, Estimated correctness of the model 97.8 % 2 chains (75 residues) have been docked in sequence Building loops using Loopy2018 7 chains (134 residues) following loop building 2 chains (75 residues) in sequence following loop building ------------------------------------------------------ 12083 reflections ( 99.83 % complete ) and 2328 restraints for refining 1527 atoms. 1502 conditional restraints added. Observations/parameters ratio is 1.98 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3130 (Rfree = 0.000) for 1527 atoms. Found 17 (37 requested) and removed 24 (22 requested) atoms. Cycle 22: After refmac, R = 0.3035 (Rfree = 0.000) for 1516 atoms. Found 13 (36 requested) and removed 22 (22 requested) atoms. Cycle 23: After refmac, R = 0.2910 (Rfree = 0.000) for 1501 atoms. Found 9 (34 requested) and removed 21 (22 requested) atoms. Cycle 24: After refmac, R = 0.2855 (Rfree = 0.000) for 1485 atoms. Found 12 (33 requested) and removed 17 (22 requested) atoms. Cycle 25: After refmac, R = 0.2834 (Rfree = 0.000) for 1479 atoms. Found 8 (33 requested) and removed 9 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.30 2.46 Round 1: 139 peptides, 9 chains. Longest chain 33 peptides. Score 0.830 Round 2: 145 peptides, 8 chains. Longest chain 45 peptides. Score 0.859 Round 3: 141 peptides, 10 chains. Longest chain 36 peptides. Score 0.821 Round 4: 144 peptides, 9 chains. Longest chain 36 peptides. Score 0.843 Round 5: 135 peptides, 11 chains. Longest chain 25 peptides. Score 0.785 Taking the results from Round 2 Chains 10, Residues 137, Estimated correctness of the model 97.7 % 4 chains (97 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 66 A and 69 A 9 chains (139 residues) following loop building 3 chains (99 residues) in sequence following loop building ------------------------------------------------------ 12083 reflections ( 99.83 % complete ) and 2065 restraints for refining 1520 atoms. 1105 conditional restraints added. Observations/parameters ratio is 1.99 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2995 (Rfree = 0.000) for 1520 atoms. Found 22 (32 requested) and removed 24 (22 requested) atoms. Cycle 27: After refmac, R = 0.2919 (Rfree = 0.000) for 1514 atoms. Found 17 (31 requested) and removed 22 (22 requested) atoms. Cycle 28: After refmac, R = 0.2833 (Rfree = 0.000) for 1506 atoms. Found 11 (30 requested) and removed 19 (22 requested) atoms. Cycle 29: After refmac, R = 0.2813 (Rfree = 0.000) for 1495 atoms. Found 10 (29 requested) and removed 14 (22 requested) atoms. Cycle 30: After refmac, R = 0.2815 (Rfree = 0.000) for 1487 atoms. Found 11 (28 requested) and removed 11 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.29 2.45 Round 1: 142 peptides, 8 chains. Longest chain 43 peptides. Score 0.852 Round 2: 144 peptides, 8 chains. Longest chain 59 peptides. Score 0.857 Round 3: 153 peptides, 10 chains. Longest chain 37 peptides. Score 0.852 Round 4: 153 peptides, 12 chains. Longest chain 35 peptides. Score 0.826 Round 5: 157 peptides, 10 chains. Longest chain 45 peptides. Score 0.862 Taking the results from Round 5 Chains 10, Residues 147, Estimated correctness of the model 97.8 % 4 chains (106 residues) have been docked in sequence Building loops using Loopy2018 10 chains (147 residues) following loop building 4 chains (106 residues) in sequence following loop building ------------------------------------------------------ 12083 reflections ( 99.83 % complete ) and 2096 restraints for refining 1531 atoms. 1096 conditional restraints added. Observations/parameters ratio is 1.97 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2986 (Rfree = 0.000) for 1531 atoms. Found 28 (28 requested) and removed 25 (22 requested) atoms. Cycle 32: After refmac, R = 0.2804 (Rfree = 0.000) for 1532 atoms. Found 18 (27 requested) and removed 20 (22 requested) atoms. Cycle 33: After refmac, R = 0.2713 (Rfree = 0.000) for 1525 atoms. Found 21 (26 requested) and removed 6 (22 requested) atoms. Cycle 34: After refmac, R = 0.2630 (Rfree = 0.000) for 1537 atoms. Found 13 (26 requested) and removed 9 (22 requested) atoms. Cycle 35: After refmac, R = 0.2616 (Rfree = 0.000) for 1540 atoms. Found 12 (25 requested) and removed 8 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.27 2.43 Round 1: 147 peptides, 7 chains. Longest chain 34 peptides. Score 0.876 Round 2: 151 peptides, 8 chains. Longest chain 34 peptides. Score 0.873 Round 3: 143 peptides, 11 chains. Longest chain 35 peptides. Score 0.811 Round 4: 154 peptides, 7 chains. Longest chain 65 peptides. Score 0.890 Round 5: 153 peptides, 10 chains. Longest chain 38 peptides. Score 0.852 Taking the results from Round 4 Chains 11, Residues 147, Estimated correctness of the model 98.5 % 4 chains (123 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 109 A and 114 A 9 chains (149 residues) following loop building 3 chains (127 residues) in sequence following loop building ------------------------------------------------------ 12083 reflections ( 99.83 % complete ) and 1875 restraints for refining 1531 atoms. 770 conditional restraints added. Observations/parameters ratio is 1.97 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2875 (Rfree = 0.000) for 1531 atoms. Found 24 (24 requested) and removed 24 (22 requested) atoms. Cycle 37: After refmac, R = 0.2730 (Rfree = 0.000) for 1530 atoms. Found 23 (23 requested) and removed 22 (22 requested) atoms. Cycle 38: After refmac, R = 0.2649 (Rfree = 0.000) for 1530 atoms. Found 16 (22 requested) and removed 18 (22 requested) atoms. Cycle 39: After refmac, R = 0.2607 (Rfree = 0.000) for 1527 atoms. Found 13 (22 requested) and removed 10 (22 requested) atoms. Cycle 40: After refmac, R = 0.2580 (Rfree = 0.000) for 1527 atoms. Found 15 (22 requested) and removed 9 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.27 2.43 Round 1: 150 peptides, 6 chains. Longest chain 36 peptides. Score 0.894 Round 2: 152 peptides, 6 chains. Longest chain 105 peptides. Score 0.897 Round 3: 150 peptides, 7 chains. Longest chain 45 peptides. Score 0.882 Round 4: 146 peptides, 5 chains. Longest chain 70 peptides. Score 0.897 Round 5: 149 peptides, 7 chains. Longest chain 51 peptides. Score 0.880 Taking the results from Round 4 Chains 7, Residues 141, Estimated correctness of the model 98.7 % 4 chains (128 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 114 A and 119 A Built loop between residues 142 A and 153 A 4 chains (148 residues) following loop building 2 chains (142 residues) in sequence following loop building ------------------------------------------------------ 12083 reflections ( 99.83 % complete ) and 1794 restraints for refining 1543 atoms. 630 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2791 (Rfree = 0.000) for 1543 atoms. Found 22 (22 requested) and removed 22 (22 requested) atoms. Cycle 42: After refmac, R = 0.2661 (Rfree = 0.000) for 1541 atoms. Found 20 (22 requested) and removed 22 (22 requested) atoms. Cycle 43: After refmac, R = 0.2591 (Rfree = 0.000) for 1539 atoms. Found 19 (22 requested) and removed 14 (22 requested) atoms. Cycle 44: After refmac, R = 0.2515 (Rfree = 0.000) for 1543 atoms. Found 10 (22 requested) and removed 13 (22 requested) atoms. Cycle 45: After refmac, R = 0.2495 (Rfree = 0.000) for 1540 atoms. Found 14 (22 requested) and removed 14 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.27 2.43 Round 1: 156 peptides, 4 chains. Longest chain 61 peptides. Score 0.923 Round 2: 153 peptides, 6 chains. Longest chain 69 peptides. Score 0.899 Round 3: 155 peptides, 5 chains. Longest chain 60 peptides. Score 0.912 Round 4: 153 peptides, 7 chains. Longest chain 44 peptides. Score 0.888 Round 5: 159 peptides, 8 chains. Longest chain 51 peptides. Score 0.888 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 152, Estimated correctness of the model 99.2 % 4 chains (149 residues) have been docked in sequence Sequence coverage is 97 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 104 A and 109 A Built loop between residues 168 A and 177 A 3 chains (164 residues) following loop building 2 chains (161 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 12083 reflections ( 99.83 % complete ) and 1298 restraints for refining 1272 atoms. Observations/parameters ratio is 2.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3287 (Rfree = 0.000) for 1272 atoms. Found 8 (18 requested) and removed 0 (18 requested) atoms. Cycle 47: After refmac, R = 0.3134 (Rfree = 0.000) for 1272 atoms. Found 7 (19 requested) and removed 0 (19 requested) atoms. Cycle 48: After refmac, R = 0.3005 (Rfree = 0.000) for 1272 atoms. Found 6 (19 requested) and removed 1 (19 requested) atoms. Cycle 49: After refmac, R = 0.2916 (Rfree = 0.000) for 1272 atoms. TimeTaking 30.73